Installation problem ESYS on fedora 20
Hey!
I got through all the installation process after following the instructions on https:/
I try to install the current stable ESyS particle version on Fedora 20 (Heisenbug, 64bit). When running the make command I receive the following error (some lines before I added):
...
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
../tml/
LatticeMaster.
../tml/
MPI_
../tml/
MPI_
../tml/
MPI_
../tml/
../tml/
LatticeMaster.
../tml/
MPI_
../tml/
MPI_
../tml/
MPI_
make[2]: *** [LatticeMaster.lo] Fehler 1
make[2]: Leaving directory `/home/
make[1]: *** [all-recursive] Fehler 1
make[1]: Leaving directory `/home/
make: *** [all] Fehler 2
Thank you very much for your help!
Djamil
Question information
- Language:
- English Edit question
- Status:
- Solved
- Assignee:
- No assignee Edit question
- Solved by:
- Vince Boros
- Solved:
- Last query:
- Last reply:
Revision history for this message
|
#1 |
Hello Djamil.
I am unsure what the error is. As far as I can see, the output that you posted shows only deprecation warnings. They should not be a problem for compilation as far as I understand. Check which C++ compiler and MPI implementation you are using. Maybe changing these will allow "make" to complete. If your problem persists, perhaps one of the developers can install Fedora on a virtual machine to replicate it.
Regards,
Vince
Revision history for this message
|
#2 |
Hi Djamil,
which MPI is this? Looking at the warnings is appears to be OpenMPI, but which version?
A quick look through the code shows that there are indeed MPI functions used which are deprecated in recent MPI versions, but as Vince said this shouldn't cause the make process to terminate - unless the compiler is using the -Werror flag, but that isn't a good idea when building esys-particle anyway ( esys-particle will not build without warnings).
Can you post the output from the make process from the last compiler call (included) to the end?
Steffen
Revision history for this message
|
#3 |
Thank you for the answers! i use the most recent versions of gcc and openmpi for fedora 20 64 bit, e.g. 1.7.3-1 for mpicc and 4.8.2-7 for gcc. Possibly it has to do with deleted functions. I tried to use the supported compilerversions but in the current fedora version they are not supported anymore and going through the library stuff to install an older version and its dependencies will be a bigger issue.
One option could be downgrading to fedora 19 or 18 but this would be a last option for me.
Using the configure command I also get some "no" after certain checkings, but it runs through without an error.
I post the output here:
[djamil@localhost ESyS]$ ./configure CC=mpicc CXX=mpic++
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for a Python interpreter with version >= 2.6... python
checking for python... /usr/bin/python
checking for python version... 2.7
checking for python platform... linux2
checking for python script directory... ${prefix}
checking for python extension module directory... ${exec_
checking build system type... x86_64-
checking host system type... x86_64-
checking how to print strings... printf
checking for style of include used by make... GNU
checking for gcc... mpicc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether mpicc accepts -g... yes
checking for mpicc option to accept ISO C89... none needed
checking dependency style of mpicc... gcc3
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by mpicc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert x86_64-
checking how to convert x86_64-
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking whether we are using the GNU C++ compiler... yes
checking whether mpic++ accepts -g... yes
checking dependency style of mpic++... gcc3
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from mpicc object... ok
checking for sysroot... no
checking for mt... no
checking if : is a manifest tool... no
checking how to run the C preprocessor... mpicc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if mpicc supports -fno-rtti -fno-exceptions... no
checking for mpicc option to produce PIC... -fPIC -DPIC
checking if mpicc PIC flag -fPIC -DPIC works... yes
checking if mpicc static flag -static works... no
checking if mpicc supports -c -o file.o... yes
checking if mpicc supports -c -o file.o... (cached) yes
checking whether the mpicc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for shl_load... no
checking for shl_load in -ldld... no
checking for dlopen... no
checking for dlopen in -ldl... yes
checking whether a program can dlopen itself... yes
checking whether a statically linked program can dlopen itself... yes
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking how to run the C++ preprocessor... mpic++ -E
checking for ld used by mpic++... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the mpic++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for mpic++ option to produce PIC... -fPIC -DPIC
checking if mpic++ PIC flag -fPIC -DPIC works... yes
checking if mpic++ static flag -static works... no
checking if mpic++ supports -c -o file.o... yes
checking if mpic++ supports -c -o file.o... (cached) yes
checking whether the mpic++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
configure: VTK support disabled
checking for povray... no
configure: POV-Ray support disabled
configure: HTML documentation disabled.
configure: PDF documentation disabled.
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether mpic++ accepts -g... (cached) yes
checking dependency style of mpic++... (cached) gcc3
checking whether we are using the GNU C compiler... (cached) yes
checking whether mpicc accepts -g... (cached) yes
checking for mpicc option to accept ISO C89... (cached) none needed
checking dependency style of mpicc... (cached) gcc3
checking how to run the C preprocessor... mpicc -E
checking for flex... no
checking for lex... no
checking for bison... no
checking for byacc... no
checking whether ln -s works... yes
checking for cp... cp -f
checking for find... find
checking for laminfo... no
7
checking for Py_Main in -lpython2.7... yes
checking for Boost headers version >= 1.34.1... yes
checking for Boost's header version... 1_54
checking for the toolset name used by Boost for mpic++... configure: WARNING: could not figure out which toolset name to use for mpic++
checking boost/system/
checking boost/system/
checking for boost/system/
checking for the Boost system library... yes
checking boost/filesyste
checking boost/filesyste
checking for boost/filesyste
checking for the Boost filesystem library... yes
checking boost/python.hpp usability... yes
checking boost/python.hpp presence... yes
checking for boost/python.hpp... yes
checking for the Boost python library... yes
checking for DBClose in -lsiloh5... no
checking for DBClose in -lsilo... no
configure: WARNING:
The SILO library was not found. SILO output will not be available.
checking for ANSI C header files... (cached) yes
checking for sys/wait.h that is POSIX.1 compatible... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... no
checking whether time.h and sys/time.h may both be included... yes
checking arpa/inet.h usability... yes
checking arpa/inet.h presence... yes
checking for arpa/inet.h... yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking hash_map usability... yes
checking hash_map presence... yes
checking for hash_map... yes
checking malloc.h usability... yes
checking malloc.h presence... yes
checking for malloc.h... yes
checking mpi.h usability... yes
checking mpi.h presence... yes
checking for mpi.h... yes
checking netdb.h usability... yes
checking netdb.h presence... yes
checking for netdb.h... yes
checking netinet/in.h usability... yes
checking netinet/in.h presence... yes
checking for netinet/in.h... yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking sys/ioctl.h usability... yes
checking sys/ioctl.h presence... yes
checking for sys/ioctl.h... yes
checking asm/ioctls.h usability... yes
checking asm/ioctls.h presence... yes
checking for asm/ioctls.h... yes
checking sys/socket.h usability... yes
checking sys/socket.h presence... yes
checking for sys/socket.h... yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for size_t... yes
checking whether mpicc needs -traditional... no
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... no
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... no
checking for working strtod... no
checking for pow... yes
checking for vprintf... yes
checking for _doprnt... no
checking for bzero... yes
checking for floor... yes
checking for gethostbyname... yes
checking for gettimeofday... yes
checking for memset... yes
checking for pow... (cached) yes
checking for socket... yes
checking for sqrt... yes
checking for strdup... yes
checking for strerror... yes
checking for strtol... yes
checking for MPI_Init... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating ntable/src/Makefile
config.status: creating ntable/Makefile
config.status: creating tml/comm/Makefile
config.status: creating tml/message/
config.status: creating tml/type/Makefile
config.status: creating tml/Makefile
config.status: creating ppa/src/Makefile
config.status: creating ppa/Makefile
config.status: creating pis/Makefile
config.status: creating Foundation/Makefile
config.status: creating Geometry/Makefile
config.status: creating Model/Makefile
config.status: creating Parallel/Makefile
config.status: creating Fields/Makefile
config.status: creating Tools/Makefile
config.status: creating Tools/dump2geo/
config.status: creating Tools/dump2pov/
config.status: creating Tools/mesh2pov/
config.status: creating Tools/rotextrac
config.status: creating Tools/StressCal
config.status: creating Tools/ExtractGr
config.status: creating Tools/dump2silo
config.status: creating Tools/dump2vtk/
config.status: creating Tools/ExtractFr
config.status: creating Tools/ForceChai
config.status: creating Tools/ExtractSt
config.status: creating Python/Makefile
config.status: creating Python/
config.status: creating Python/
config.status: creating Python/
config.status: creating Python/
config.status: creating Python/
config.status: creating Python/
config.status: creating Python/
config.status: creating Python/
config.status: creating Python/
config.status: creating Python/
config.status: creating Python/
config.status: creating Doc/Tutorial/
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
=== configuring in libltdl (/home/
configure: running /bin/sh ./configure --disable-
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking build system type... x86_64-
checking host system type... x86_64-
checking how to print strings... printf
checking for style of include used by make... GNU
checking for gcc... mpicc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether mpicc accepts -g... yes
checking for mpicc option to accept ISO C89... none needed
checking dependency style of mpicc... gcc3
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by mpicc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert x86_64-
checking how to convert x86_64-
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from mpicc object... ok
checking for sysroot... no
checking for mt... no
checking if : is a manifest tool... no
checking how to run the C preprocessor... mpicc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if mpicc supports -fno-rtti -fno-exceptions... no
checking for mpicc option to produce PIC... -fPIC -DPIC
checking if mpicc PIC flag -fPIC -DPIC works... yes
checking if mpicc static flag -static works... no
checking if mpicc supports -c -o file.o... yes
checking if mpicc supports -c -o file.o... (cached) yes
checking whether the mpicc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for shl_load... no
checking for shl_load in -ldld... no
checking for dlopen... no
checking for dlopen in -ldl... yes
checking whether a program can dlopen itself... yes
checking whether a statically linked program can dlopen itself... yes
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking which extension is used for runtime loadable modules... .so
checking which variable specifies run-time module search path... LD_LIBRARY_PATH
checking for the default library search path... /lib64 /usr/lib64 /lib /usr/lib /usr/lib64/atlas /usr/lib64/iscsi /usr/lib64/llvm /usr/lib64/mysql /usr/lib/
checking for library containing dlopen... -ldl
checking for dlerror... yes
checking for shl_load... (cached) no
checking for shl_load in -ldld... (cached) no
checking for dld_link in -ldld... no
checking for _ prefix in compiled symbols... no
checking whether deplibs are loaded by dlopen... yes
checking for argz.h... yes
checking for error_t... yes
checking for argz_add... yes
checking for argz_append... yes
checking for argz_count... yes
checking for argz_create_sep... yes
checking for argz_insert... yes
checking for argz_next... yes
checking for argz_stringify... yes
checking if argz actually works... yes
checking whether libtool supports -dlopen/
checking for unistd.h... (cached) yes
checking for dl.h... no
checking for sys/dl.h... no
checking for dld.h... no
checking for mach-o/dyld.h... no
checking for dirent.h... yes
checking for closedir... yes
checking for opendir... yes
checking for readdir... yes
checking for strlcat... no
checking for strlcpy... no
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
In the next message I post the complete make install output.
Revision history for this message
|
#4 |
Here the make output:
make all-recursive
make[1]: Entering directory `/home/
Making all in libltdl
make[2]: Entering directory `/home/
make all-am
make[3]: Entering directory `/home/
/bin/sh ./libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H -I. -DLT_CONFIG_
libtool: compile: mpicc -DHAVE_CONFIG_H -I. "-DLT_CONFIG_
libtool: compile: mpicc -DHAVE_CONFIG_H -I. "-DLT_CONFIG_
mv -f .deps/dlopen.Tpo .deps/dlopen.Plo
/bin/sh ./libtool --tag=CC --mode=link mpicc -g -O2 -module -avoid-version -o dlopen.la dlopen.lo -ldl -ldl
libtool: link: ar cru .libs/dlopen.a .libs/dlopen.o
libtool: link: ranlib .libs/dlopen.a
libtool: link: ( cd ".libs" && rm -f "dlopen.la" && ln -s "../dlopen.la" "dlopen.la" )
/bin/sh ./libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc -DLT_CONFIG_
libtool: compile: mpicc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_
libtool: compile: mpicc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_
mv -f .deps/libltdlc_
/bin/sh ./libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc -DLT_CONFIG_
libtool: compile: mpicc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_
libtool: compile: mpicc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_
mv -f .deps/libltdlc_
/bin/sh ./libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc -DLT_CONFIG_
libtool: compile: mpicc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_
libtool: compile: mpicc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_
mv -f .deps/libltdlc_
/bin/sh ./libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc -DLT_CONFIG_
libtool: compile: mpicc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_
libtool: compile: mpicc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_
mv -f .deps/libltdlc_
/bin/sh ./libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc -DLT_CONFIG_
libtool: compile: mpicc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_
libtool: compile: mpicc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_
mv -f .deps/libltdlc_
/bin/sh ./libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc -DLT_CONFIG_
libtool: compile: mpicc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_
libtool: compile: mpicc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_
mv -f .deps/libltdlc_
/bin/sh ./libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H -I. -DLT_CONFIG_
libtool: compile: mpicc -DHAVE_CONFIG_H -I. "-DLT_CONFIG_
libtool: compile: mpicc -DHAVE_CONFIG_H -I. "-DLT_CONFIG_
mv -f .deps/lt__strl.Tpo .deps/lt__strl.Plo
/bin/sh ./libtool --tag=CC --mode=link mpicc -g -O2 -no-undefined -dlpreopen dlopen.la -o libltdlc.la libltdlc_
libtool: link: rm -f .libs/libltdlc.nm .libs/libltdlc.nmS .libs/libltdlc.nmT
libtool: link: (cd .libs && mpicc -g -O2 -c -fno-builtin -fPIC -DPIC "libltdlcS.c")
libtool: link: rm -f ".libs/libltdlcS.c" ".libs/libltdlc.nm" ".libs/
libtool: link: (cd .libs/libltdlc.
libtool: link: ar cru .libs/libltdlc.a .libs/libltdlc_
libtool: link: ranlib .libs/libltdlc.a
libtool: link: rm -fr .libs/libltdlc.lax
libtool: link: ( cd ".libs" && rm -f "libltdlc.la" && ln -s "../libltdlc.la" "libltdlc.la" )
make[3]: Leaving directory `/home/
make[2]: Leaving directory `/home/
Making all in Foundation
make[2]: Entering directory `/home/
/bin/sh ../libtool --tag=CXX --mode=compile mpic++ -DHAVE_CONFIG_H -I. -I.. "-I.." -I/usr/
libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/
libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/
mv -f .deps/libFounda
/bin/sh ../libtool --tag=CXX --mode=compile mpic++ -DHAVE_CONFIG_H -I. -I.. "-I.." -I/usr/
libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/
libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/
mv -f .deps/libFounda
/bin/sh ../libtool --tag=CXX --mode=compile mpic++ -DHAVE_CONFIG_H -I. -I.. "-I.." -I/usr/
libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/
libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/
mv -f .deps/libFounda
/bin/sh ../libtool --tag=CXX --mode=compile mpic++ -DHAVE_CONFIG_H -I. -I.. "-I.." -I/usr/
libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/
libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/
mv -f .deps/libFounda
/bin/sh ../libtool --tag=CXX --mode=compile mpic++ -DHAVE_CONFIG_H -I. -I.. "-I.." -I/usr/
libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/
libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/
mv -f .deps/libFounda
/bin/sh ../libtool --tag=CXX --mode=compile mpic++ -DHAVE_CONFIG_H -I. -I.. "-I.." -I/usr/
libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/
libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/
mv -f .deps/libFounda
/bin/sh ../libtool --tag=CXX --mode=compile mpic++ -DHAVE_CONFIG_H -I. -I.. "-I.." -I/usr/
libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/
libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/
mv -f .deps/libFounda
/bin/sh ../libtool --tag=CXX --mode=compile mpic++ -DHAVE_CONFIG_H -I. -I.. "-I.." -I/usr/
libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/
libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/
mv -f .deps/libFounda
/bin/sh ../libtool --tag=CXX --mode=compile mpic++ -DHAVE_CONFIG_H -I. -I.. "-I.." -I/usr/
libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/
libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/
mv -f .deps/libFounda
/bin/sh ../libtool --tag=CXX --mode=compile mpic++ -DHAVE_CONFIG_H -I. -I.. "-I.." -I/usr/
libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/
libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/
mv -f .deps/libFounda
/bin/sh ../libtool --tag=CXX --mode=compile mpic++ -DHAVE_CONFIG_H -I. -I.. "-I.." -I/usr/
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libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Foundation -I../Parallel -I../Fields -I../Parser -g -O2 -MT Mesh2DReaderImpl.lo -MD -MP -MF .deps/Mesh2DRea
mv -f .deps/Mesh2DRea
/bin/sh ../libtool --tag=CXX --mode=compile mpic++ -DHAVE_CONFIG_H -I. -I.. "-I.." -I../Foundation -I../Parallel -I../Fields -I../Parser -g -O2 -MT MeshReader.lo -MD -MP -MF .deps/MeshReade
libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Foundation -I../Parallel -I../Fields -I../Parser -g -O2 -MT MeshReader.lo -MD -MP -MF .deps/MeshReade
libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Foundation -I../Parallel -I../Fields -I../Parser -g -O2 -MT MeshReader.lo -MD -MP -MF .deps/MeshReade
mv -f .deps/MeshReade
/bin/sh ../libtool --tag=CXX --mode=compile mpic++ -DHAVE_CONFIG_H -I. -I.. "-I.." -I../Foundation -I../Parallel -I../Fields -I../Parser -g -O2 -MT MeshReaderImpl.lo -MD -MP -MF .deps/MeshReade
libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Foundation -I../Parallel -I../Fields -I../Parser -g -O2 -MT MeshReaderImpl.lo -MD -MP -MF .deps/MeshReade
libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Foundation -I../Parallel -I../Fields -I../Parser -g -O2 -MT MeshReaderImpl.lo -MD -MP -MF .deps/MeshReade
mv -f .deps/MeshReade
/bin/sh ../libtool --tag=CXX --mode=compile mpic++ -DHAVE_CONFIG_H -I. -I.. "-I.." -I../Foundation -I../Parallel -I../Fields -I../Parser -g -O2 -MT vec3_mpi.lo -MD -MP -MF .deps/vec3_mpi.Tpo -c -o vec3_mpi.lo `test -f '../Parallel/
libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Foundation -I../Parallel -I../Fields -I../Parser -g -O2 -MT vec3_mpi.lo -MD -MP -MF .deps/vec3_mpi.Tpo -c ../Parallel/
libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Foundation -I../Parallel -I../Fields -I../Parser -g -O2 -MT vec3_mpi.lo -MD -MP -MF .deps/vec3_mpi.Tpo -c ../Parallel/
mv -f .deps/vec3_mpi.Tpo .deps/vec3_mpi.Plo
/bin/sh ../libtool --tag=CXX --mode=link mpic++ -g -O2 -release 2.3 -L/usr/lib -o libModel.la -rpath /usr/local/lib ABCDampingIGP.lo AdhesiveFriction.lo BasicParticle.lo BodyForceGroup.lo BondedInteracti
libtool: link: mpic++ -fPIC -DPIC -shared -nostdlib /usr/lib64/
libtool: link: (cd ".libs" && rm -f "libModel.so" && ln -s "libModel-2.3.so" "libModel.so")
libtool: link: ar cru .libs/libModel.a ABCDampingIGP.o AdhesiveFriction.o BasicParticle.o BodyForceGroup.o BondedInteraction.o BTriangleIntera
libtool: link: ranlib .libs/libModel.a
libtool: link: ( cd ".libs" && rm -f "libModel.la" && ln -s "../libModel.la" "libModel.la" )
make[2]: Leaving directory `/home/
Making all in Fields
make[2]: Entering directory `/home/
/bin/sh ../libtool --tag=CXX --mode=compile mpic++ -DHAVE_CONFIG_H -I. -I.. "-I.." -I../Foundation -I../Model -g -O2 -MT InteractionFiel
libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Foundation -I../Model -g -O2 -MT InteractionFiel
libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Foundation -I../Model -g -O2 -MT InteractionFiel
mv -f .deps/Interacti
/bin/sh ../libtool --tag=CXX --mode=compile mpic++ -DHAVE_CONFIG_H -I. -I.. "-I.." -I../Foundation -I../Model -g -O2 -MT ParticleFieldMa
libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Foundation -I../Model -g -O2 -MT ParticleFieldMa
libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Foundation -I../Model -g -O2 -MT ParticleFieldMa
mv -f .deps/ParticleF
/bin/sh ../libtool --tag=CXX --mode=compile mpic++ -DHAVE_CONFIG_H -I. -I.. "-I.." -I../Foundation -I../Model -g -O2 -MT TriggeredVector
libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Foundation -I../Model -g -O2 -MT TriggeredVector
libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Foundation -I../Model -g -O2 -MT TriggeredVector
mv -f .deps/Triggered
/bin/sh ../libtool --tag=CXX --mode=compile mpic++ -DHAVE_CONFIG_H -I. -I.. "-I.." -I../Foundation -I../Model -g -O2 -MT ScalarParticleD
libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Foundation -I../Model -g -O2 -MT ScalarParticleD
libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Foundation -I../Model -g -O2 -MT ScalarParticleD
mv -f .deps/ScalarPar
/bin/sh ../libtool --tag=CXX --mode=compile mpic++ -DHAVE_CONFIG_H -I. -I.. "-I.." -I../Foundation -I../Model -g -O2 -MT ScalarTriangleF
libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Foundation -I../Model -g -O2 -MT ScalarTriangleF
libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Foundation -I../Model -g -O2 -MT ScalarTriangleF
mv -f .deps/ScalarTri
/bin/sh ../libtool --tag=CXX --mode=compile mpic++ -DHAVE_CONFIG_H -I. -I.. "-I.." -I../Foundation -I../Model -g -O2 -MT ScalarTriangleF
libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Foundation -I../Model -g -O2 -MT ScalarTriangleF
libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Foundation -I../Model -g -O2 -MT ScalarTriangleF
mv -f .deps/ScalarTri
/bin/sh ../libtool --tag=CXX --mode=compile mpic++ -DHAVE_CONFIG_H -I. -I.. "-I.." -I../Foundation -I../Model -g -O2 -MT VectorInteracti
libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Foundation -I../Model -g -O2 -MT VectorInteracti
libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Foundation -I../Model -g -O2 -MT VectorInteracti
mv -f .deps/VectorInt
/bin/sh ../libtool --tag=CXX --mode=compile mpic++ -DHAVE_CONFIG_H -I. -I.. "-I.." -I../Foundation -I../Model -g -O2 -MT VectorTriangleF
libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Foundation -I../Model -g -O2 -MT VectorTriangleF
libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Foundation -I../Model -g -O2 -MT VectorTriangleF
mv -f .deps/VectorTri
/bin/sh ../libtool --tag=CXX --mode=compile mpic++ -DHAVE_CONFIG_H -I. -I.. "-I.." -I../Foundation -I../Model -g -O2 -MT VectorTriangleF
libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Foundation -I../Model -g -O2 -MT VectorTriangleF
libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Foundation -I../Model -g -O2 -MT VectorTriangleF
mv -f .deps/VectorTri
/bin/sh ../libtool --tag=CXX --mode=compile mpic++ -DHAVE_CONFIG_H -I. -I.. "-I.." -I../Foundation -I../Model -g -O2 -MT VectorEdge2DFie
libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Foundation -I../Model -g -O2 -MT VectorEdge2DFie
libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Foundation -I../Model -g -O2 -MT VectorEdge2DFie
mv -f .deps/VectorEdg
/bin/sh ../libtool --tag=CXX --mode=compile mpic++ -DHAVE_CONFIG_H -I. -I.. "-I.." -I../Foundation -I../Model -g -O2 -MT MaxTrigger.lo -MD -MP -MF .deps/MaxTrigge
libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Foundation -I../Model -g -O2 -MT MaxTrigger.lo -MD -MP -MF .deps/MaxTrigge
libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Foundation -I../Model -g -O2 -MT MaxTrigger.lo -MD -MP -MF .deps/MaxTrigge
mv -f .deps/MaxTrigge
/bin/sh ../libtool --tag=CXX --mode=link mpic++ -g -O2 -release 2.3 -L/usr/lib -o libFields.la -rpath /usr/local/lib InteractionFiel
libtool: link: mpic++ -fPIC -DPIC -shared -nostdlib /usr/lib64/
libtool: link: (cd ".libs" && rm -f "libFields.so" && ln -s "libFields-2.3.so" "libFields.so")
libtool: link: ar cru .libs/libFields.a InteractionFiel
libtool: link: ranlib .libs/libFields.a
libtool: link: ( cd ".libs" && rm -f "libFields.la" && ln -s "../libFields.la" "libFields.la" )
make[2]: Leaving directory `/home/
Making all in Parallel
make[2]: Entering directory `/home/
/bin/sh ../libtool --tag=CXX --mode=compile mpic++ -DHAVE_CONFIG_H -I. -I.. "-I.." -I.. -I../Foundation -I../Model -I../Fields -I../Interface -I../MainBE -I../Socket -g -O2 -MT ASubLattice.lo -MD -MP -MF .deps/ASubLatti
libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I.. -I../Foundation -I../Model -I../Fields -I../Interface -I../MainBE -I../Socket -g -O2 -MT ASubLattice.lo -MD -MP -MF .deps/ASubLatti
libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I.. -I../Foundation -I../Model -I../Fields -I../Interface -I../MainBE -I../Socket -g -O2 -MT ASubLattice.lo -MD -MP -MF .deps/ASubLatti
mv -f .deps/ASubLatti
/bin/sh ../libtool --tag=CXX --mode=compile mpic++ -DHAVE_CONFIG_H -I. -I.. "-I.." -I.. -I../Foundation -I../Model -I../Fields -I../Interface -I../MainBE -I../Socket -g -O2 -MT LatticeMaster.lo -MD -MP -MF .deps/LatticeMa
libtool: compile: mpic++ -DHAVE_CONFIG_H -I. -I.. -I.. -I.. -I../Foundation -I../Model -I../Fields -I../Interface -I../MainBE -I../Socket -g -O2 -MT LatticeMaster.lo -MD -MP -MF .deps/LatticeMa
make[2]: Leaving directory `/home/
make[1]: Leaving directory `/home/
Revision history for this message
|
#5 |
And here the warnings (not all of them, would be too much):
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
In file included from ../tml/
../tml/
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
../tml/
ScalarTriangleF
../tml/
MPI_
../tml/
MPI_
../tml/
MPI_
In file included from ../tml/
../tml/
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
../tml/
ScalarTriangleF
../tml/
MPI_
../tml/
MPI_
../tml/
MPI_
In file included from ../tml/
../tml/
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
../tml/
VectorInteracti
../tml/
MPI_
../tml/
MPI_
../tml/
MPI_
../tml/
../tml/
VectorInteracti
../tml/
MPI_
../tml/
MPI_
../tml/
MPI_
../tml/
../tml/
VectorInteracti
../tml/
MPI_
../tml/
MPI_
../tml/
MPI_
../tml/
../tml/
VectorInteracti
../tml/
MPI_
../tml/
MPI_
../tml/
MPI_
../tml/
../tml/
../tml/
VectorInteracti
../tml/
MPI_
../tml/
MPI_
../tml/
MPI_
../tml/
MPI_
../tml/
../tml/
../tml/
VectorInteracti
../tml/
MPI_
../tml/
MPI_
../tml/
MPI_
../tml/
MPI_
../tml/
MPI_
../tml/
MPI_
../tml/
../tml/
../tml/
VectorInteracti
../tml/
MPI_
../tml/
MPI_
../tml/
MPI_
../tml/
MPI_
../tml/
MPI_
../tml/
MPI_
In file included from ../tml/
../tml/
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
../tml/
VectorTriangleF
../tml/
MPI_
../tml/
MPI_
../tml/
MPI_
In file included from ../tml/
../tml/
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
../tml/
VectorTriangleF
../tml/
MPI_
../tml/
MPI_
../tml/
MPI_
In file included from ../tml/
../tml/
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
../tml/
VectorEdge2DFie
../tml/
MPI_
../tml/
MPI_
../tml/
MPI_
In file included from ../tml/
../tml/
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
In file included from /usr/local/
/usr/include/
using ::malloc;
^
/usr/include/
using ::realloc;
^
In file included from ../tml/
../tml/
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
MPI_
^
../tml/
../tml/
LatticeMaster.
../tml/
MPI_
../tml/
MPI_
../tml/
MPI_
../tml/
../tml/
LatticeMaster.
../tml/
MPI_
../tml/
MPI_
../tml/
MPI_
make[2]: *** [LatticeMaster.lo] Fehler 1
make[1]: *** [all-recursive] Fehler 1
make: *** [all] Fehler 2
[djamil@localhost ESyS]$
Thank you very much!!
Revision history for this message
|
#6 |
Hi Djamil et al.,
It looks to me like the MPI warnings are irrelevant to the build problem here. Intermingled with all the warnings are these two error messages:
In file included from /usr/local/
/usr/include/
using ::malloc;
^
/usr/include/
using ::realloc;
This appears to be a known problem and is discussed here:
http://
Vince, could you please look into this and see what needs to be done to work around it? Might need some changes in configure.ac.
Cheers,
Dion
Revision history for this message
|
#7 |
Hello Djamil.
The errors come from two check-failures in configure:
checking for GNU libc compatible malloc... no
checking for GNU libc compatible realloc... no
This is surprising since you are using gcc. This leads me to believe that the failures may be from something else.
Following from the link Dion supplied, I would like to know whether the failed checks have to do with where libraries are installed. Assuming that you did not use the "--prefix" option on the "configure CC=mpicc CXX=mpic++" line, your library installation directory will be /usr/local/lib/. In that case run the following:
sudo make uninstall
make distclean
export LD_LIBRARY_
and then rerun your "configure" line, noting the result of the two compatibility checks above.
Let me know how you go.
Vince
Revision history for this message
|
#8 |
Hey Vince,
I tried the proposed export LD-Library_Path solution but I'm still getting the same result (see below). I didn't use the prefix option. The libraries are in /usr/local/lib, correct.
Djamil
[djamil@localhost ESyS]$ ./configure CC=mpicc CXX=mpic++
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for a Python interpreter with version >= 2.6... python
checking for python... /usr/bin/python
checking for python version... 2.7
checking for python platform... linux2
checking for python script directory... ${prefix}
checking for python extension module directory... ${exec_
checking build system type... x86_64-
checking host system type... x86_64-
checking how to print strings... printf
checking for style of include used by make... GNU
checking for gcc... mpicc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether mpicc accepts -g... yes
checking for mpicc option to accept ISO C89... none needed
checking dependency style of mpicc... gcc3
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by mpicc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert x86_64-
checking how to convert x86_64-
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking whether we are using the GNU C++ compiler... yes
checking whether mpic++ accepts -g... yes
checking dependency style of mpic++... gcc3
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from mpicc object... ok
checking for sysroot... no
checking for mt... no
checking if : is a manifest tool... no
checking how to run the C preprocessor... mpicc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if mpicc supports -fno-rtti -fno-exceptions... no
checking for mpicc option to produce PIC... -fPIC -DPIC
checking if mpicc PIC flag -fPIC -DPIC works... yes
checking if mpicc static flag -static works... no
checking if mpicc supports -c -o file.o... yes
checking if mpicc supports -c -o file.o... (cached) yes
checking whether the mpicc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for shl_load... no
checking for shl_load in -ldld... no
checking for dlopen... no
checking for dlopen in -ldl... yes
checking whether a program can dlopen itself... yes
checking whether a statically linked program can dlopen itself... yes
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking how to run the C++ preprocessor... mpic++ -E
checking for ld used by mpic++... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the mpic++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for mpic++ option to produce PIC... -fPIC -DPIC
checking if mpic++ PIC flag -fPIC -DPIC works... yes
checking if mpic++ static flag -static works... no
checking if mpic++ supports -c -o file.o... yes
checking if mpic++ supports -c -o file.o... (cached) yes
checking whether the mpic++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
configure: VTK support disabled
checking for povray... no
configure: POV-Ray support disabled
configure: HTML documentation disabled.
configure: PDF documentation disabled.
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether mpic++ accepts -g... (cached) yes
checking dependency style of mpic++... (cached) gcc3
checking whether we are using the GNU C compiler... (cached) yes
checking whether mpicc accepts -g... (cached) yes
checking for mpicc option to accept ISO C89... (cached) none needed
checking dependency style of mpicc... (cached) gcc3
checking how to run the C preprocessor... mpicc -E
checking for flex... no
checking for lex... no
checking for bison... no
checking for byacc... no
checking whether ln -s works... yes
checking for cp... cp -f
checking for find... find
checking for laminfo... no
7
checking for Py_Main in -lpython2.7... yes
checking for Boost headers version >= 1.34.1... yes
checking for Boost's header version... 1_54
checking for the toolset name used by Boost for mpic++... configure: WARNING: could not figure out which toolset name to use for mpic++
checking boost/system/
checking boost/system/
checking for boost/system/
checking for the Boost system library... yes
checking boost/filesyste
checking boost/filesyste
checking for boost/filesyste
checking for the Boost filesystem library... yes
checking boost/python.hpp usability... yes
checking boost/python.hpp presence... yes
checking for boost/python.hpp... yes
checking for the Boost python library... yes
checking for DBClose in -lsiloh5... no
checking for DBClose in -lsilo... no
configure: WARNING:
The SILO library was not found. SILO output will not be available.
checking for ANSI C header files... (cached) yes
checking for sys/wait.h that is POSIX.1 compatible... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... no
checking whether time.h and sys/time.h may both be included... yes
checking arpa/inet.h usability... yes
checking arpa/inet.h presence... yes
checking for arpa/inet.h... yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking hash_map usability... yes
checking hash_map presence... yes
checking for hash_map... yes
checking malloc.h usability... yes
checking malloc.h presence... yes
checking for malloc.h... yes
checking mpi.h usability... yes
checking mpi.h presence... yes
checking for mpi.h... yes
checking netdb.h usability... yes
checking netdb.h presence... yes
checking for netdb.h... yes
checking netinet/in.h usability... yes
checking netinet/in.h presence... yes
checking for netinet/in.h... yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking sys/ioctl.h usability... yes
checking sys/ioctl.h presence... yes
checking for sys/ioctl.h... yes
checking asm/ioctls.h usability... yes
checking asm/ioctls.h presence... yes
checking for asm/ioctls.h... yes
checking sys/socket.h usability... yes
checking sys/socket.h presence... yes
checking for sys/socket.h... yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for size_t... yes
checking whether mpicc needs -traditional... no
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... no
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... no
checking for working strtod... no
checking for pow... yes
checking for vprintf... yes
checking for _doprnt... no
checking for bzero... yes
checking for floor... yes
checking for gethostbyname... yes
checking for gettimeofday... yes
checking for memset... yes
checking for pow... (cached) yes
checking for socket... yes
checking for sqrt... yes
checking for strdup... yes
checking for strerror... yes
checking for strtol... yes
checking for MPI_Init... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating ntable/src/Makefile
config.status: creating ntable/Makefile
config.status: creating tml/comm/Makefile
config.status: creating tml/message/
config.status: creating tml/type/Makefile
config.status: creating tml/Makefile
config.status: creating ppa/src/Makefile
config.status: creating ppa/Makefile
config.status: creating pis/Makefile
config.status: creating Foundation/Makefile
config.status: creating Geometry/Makefile
config.status: creating Model/Makefile
config.status: creating Parallel/Makefile
config.status: creating Fields/Makefile
config.status: creating Tools/Makefile
config.status: creating Tools/dump2geo/
config.status: creating Tools/dump2pov/
config.status: creating Tools/mesh2pov/
config.status: creating Tools/rotextrac
config.status: creating Tools/StressCal
config.status: creating Tools/ExtractGr
config.status: creating Tools/dump2silo
config.status: creating Tools/dump2vtk/
config.status: creating Tools/ExtractFr
config.status: creating Tools/ForceChai
config.status: creating Tools/ExtractSt
config.status: creating Python/Makefile
config.status: creating Python/
config.status: creating Python/
config.status: creating Python/
config.status: creating Python/
config.status: creating Python/
config.status: creating Python/
config.status: creating Python/
config.status: creating Python/
config.status: creating Python/
config.status: creating Python/
config.status: creating Python/
config.status: creating Doc/Tutorial/
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
=== configuring in libltdl (/home/
configure: running /bin/sh ./configure --disable-
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking build system type... x86_64-
checking host system type... x86_64-
checking how to print strings... printf
checking for style of include used by make... GNU
checking for gcc... mpicc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether mpicc accepts -g... yes
checking for mpicc option to accept ISO C89... none needed
checking dependency style of mpicc... gcc3
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by mpicc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert x86_64-
checking how to convert x86_64-
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from mpicc object... ok
checking for sysroot... no
checking for mt... no
checking if : is a manifest tool... no
checking how to run the C preprocessor... mpicc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if mpicc supports -fno-rtti -fno-exceptions... no
checking for mpicc option to produce PIC... -fPIC -DPIC
checking if mpicc PIC flag -fPIC -DPIC works... yes
checking if mpicc static flag -static works... no
checking if mpicc supports -c -o file.o... yes
checking if mpicc supports -c -o file.o... (cached) yes
checking whether the mpicc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for shl_load... no
checking for shl_load in -ldld... no
checking for dlopen... no
checking for dlopen in -ldl... yes
checking whether a program can dlopen itself... yes
checking whether a statically linked program can dlopen itself... yes
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking which extension is used for runtime loadable modules... .so
checking which variable specifies run-time module search path... LD_LIBRARY_PATH
checking for the default library search path... /lib64 /usr/lib64 /lib /usr/lib /usr/lib64/atlas /usr/lib64/iscsi /usr/lib64/llvm /usr/lib64/mysql /usr/lib/
checking for library containing dlopen... -ldl
checking for dlerror... yes
checking for shl_load... (cached) no
checking for shl_load in -ldld... (cached) no
checking for dld_link in -ldld... no
checking for _ prefix in compiled symbols... no
checking whether deplibs are loaded by dlopen... yes
checking for argz.h... yes
checking for error_t... yes
checking for argz_add... yes
checking for argz_append... yes
checking for argz_count... yes
checking for argz_create_sep... yes
checking for argz_insert... yes
checking for argz_next... yes
checking for argz_stringify... yes
checking if argz actually works... yes
checking whether libtool supports -dlopen/
checking for unistd.h... (cached) yes
checking for dl.h... no
checking for sys/dl.h... no
checking for dld.h... no
checking for mach-o/dyld.h... no
checking for dirent.h... yes
checking for closedir... yes
checking for opendir... yes
checking for readdir... yes
checking for strlcat... no
checking for strlcpy... no
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
Revision history for this message
|
#9 |
In that case:
sudo make uninstall
make distclean
if you have tried to run "make", and then in configure.ac comment out these two lines:
AC_FUNC_MALLOC
AC_FUNC_REALLOC
Then run:
sh autogen.sh
configure CC=mpicc CXX=mpic++ ...
make
Look for error messages from "make". Hopefully on your system the two macros above are unnecessary and this may serve as a temporary fix.
Vince
Revision history for this message
|
#10 |
First at all thanks very much for the support!
I commented out the lines and then the configuration plus make processes went without any visible errors!
Thats a great progress!
Nevertheless when trying to run the example script bingle_output I receive the following missing module statement from Python.
[djamil@localhost Examples]$ mpirun -np 2 esysparticle bingle_output.py
CSubLatticeCont
Traceback (most recent call last):
File "bingle_output.py", line 12, in <module>
from esys.lsm import *
ImportError: No module named esys.lsm
^C[djamil@localhost Examples]$ echo $PYTHONPATH
/usr/local/
As you can see the PYTHONPATH variable is correct and also the sys.path contains the folder with the existing esys.lsm module. Do you think it has to do with the errors before that we solved via commenting out? As I remember the modules affected had something to do with LatticeMaster.lo.
Revision history for this message
|
#11 |
Hi Djamil.
What can you see in /usr/local/
You are getting close, though.
Vince
Revision history for this message
|
#12 |
Hi Djamil,
Further to Vince's suggestion, also check in /usr/local/
Some linux distributions install into dist-packages and others into site-packages. If you find the esys/lsm stuff in dist-packages, change your PYTHONPATH to look in that directory.
Cheers,
Dion
Revision history for this message
|
#13 |
Hi Vince and Dion,
sorry for answering so late. I noticed that i had python 3.3.2 installed additionally to Python 2.7.5. I removed the new version and compiled ESyS again with the same commands, again no error in ./configure or make, but with sudo make install I get the following errors ("Fehler") at the bottom and the python modules are not installed in the appropriate directory (/usr/local/
[djamil@localhost ESyS]$ sudo make install
Making install in libltdl
make[1]: Entering directory `/home/
make install-am
make[2]: Entering directory `/home/
make[3]: Entering directory `/home/
test -z "/usr/local/lib" || /usr/bin/mkdir -p "/usr/local/lib"
test -z "/usr/local/
test -z "" || /usr/bin/mkdir -p ""
make[3]: Leaving directory `/home/
make[2]: Leaving directory `/home/
make[1]: Leaving directory `/home/
Making install in Foundation
make[1]: Entering directory `/home/
make[2]: Entering directory `/home/
/usr/bin/mkdir -p '/usr/local/lib'
/bin/sh ../libtool --mode=install /usr/bin/install -c libFoundation.la '/usr/local/lib'
libtool: install: /usr/bin/install -c .libs/libFounda
libtool: install: (cd /usr/local/lib && { ln -s -f libFoundation-
libtool: install: /usr/bin/install -c .libs/libFounda
libtool: install: /usr/bin/install -c .libs/libFounda
libtool: install: chmod 644 /usr/local/
libtool: install: ranlib /usr/local/
libtool: finish: PATH="/
-------
Libraries have been installed in:
/usr/local/lib
If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
- add LIBDIR to the `LD_LIBRARY_PATH' environment variable
during execution
- add LIBDIR to the `LD_RUN_PATH' environment variable
during linking
- use the `-Wl,-rpath -Wl,LIBDIR' linker flag
- have your system administrator add LIBDIR to `/etc/ld.so.conf'
See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
-------
make[2]: Für das Ziel »install-data-am« ist nichts zu tun.
make[2]: Leaving directory `/home/
make[1]: Leaving directory `/home/
Making install in ntable
make[1]: Entering directory `/home/
Making install in src
make[2]: Entering directory `/home/
make[3]: Entering directory `/home/
/usr/bin/mkdir -p '/usr/local/lib'
/bin/sh ../../libtool --mode=install /usr/bin/install -c libntable.la '/usr/local/lib'
libtool: install: warning: relinking `libntable.la'
libtool: install: (cd /home/djamil/
libtool: relink: mpic++ -fPIC -DPIC -shared -nostdlib /usr/lib64/
/home/djamil/
libtool: install: error: relink `libntable.la' with the above command before installing it
make[3]: *** [install-
make[3]: Leaving directory `/home/
make[2]: *** [install-am] Fehler 2
make[2]: Leaving directory `/home/
make[1]: *** [install-recursive] Fehler 1
make[1]: Leaving directory `/home/
make: *** [install-recursive] Fehler 1
Revision history for this message
|
#14 |
When I use su and then make install instead I don't receive errors and the modules are all in the appropriate directory. Nevertheless I'm not able to run the bingle_output.py example with the same error mentioned before.
As user:
[djamil@localhost Examples]$ mpirun -np 2 esysparticle bingle_output.py
CSubLatticeCont
Traceback (most recent call last):
File "bingle_output.py", line 12, in <module>
from esys.lsm import *
ImportError: No module named esys.lsm
^C[djamil@localhost Examples]$
As root:
root@localhost Examples]# mpirun -np 2 esysparticle bingle_output.py
-------
Primary job terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
-------
esysparticle: error while loading shared libraries: libmpi_cxx.so.1: cannot open shared object file: No such file or directory
-------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:
Process name: [[48936,1],0]
Exit code: 127
Here the output of make install:
libtool: install: warning: relinking `libGgGeometry.la'
libtool: install: (cd /home/djamil/
libtool: relink: mpic++ -fPIC -DPIC -shared -nostdlib /usr/lib64/
libtool: install: /usr/bin/install -c .libs/libGgGeom
libtool: install: (cd /usr/local/lib && { ln -s -f libGgGeometry-
libtool: install: /usr/bin/install -c .libs/libGgGeom
libtool: install: /usr/bin/install -c .libs/libGgGeom
libtool: install: chmod 644 /usr/local/
libtool: install: ranlib /usr/local/
libtool: finish: PATH="/
-------
Libraries have been installed in:
/usr/local/lib
If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
- add LIBDIR to the `LD_LIBRARY_PATH' environment variable
during execution
- add LIBDIR to the `LD_RUN_PATH' environment variable
during linking
- use the `-Wl,-rpath -Wl,LIBDIR' linker flag
- have your system administrator add LIBDIR to `/etc/ld.so.conf'
See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
-------
make[2]: Für das Ziel »install-data-am« ist nichts zu tun.
make[2]: Leaving directory `/home/
make[1]: Leaving directory `/home/
Making install in Model
make[1]: Entering directory `/home/
make[2]: Entering directory `/home/
/usr/bin/mkdir -p '/usr/local/lib'
/bin/sh ../libtool --mode=install /usr/bin/install -c libModel.la '/usr/local/lib'
libtool: install: warning: relinking `libModel.la'
libtool: install: (cd /home/djamil/
libtool: relink: mpic++ -fPIC -DPIC -shared -nostdlib /usr/lib64/
libtool: install: /usr/bin/install -c .libs/libModel-
libtool: install: (cd /usr/local/lib && { ln -s -f libModel-2.3.so libModel.so || { rm -f libModel.so && ln -s libModel-2.3.so libModel.so; }; })
libtool: install: /usr/bin/install -c .libs/libModel.lai /usr/local/
libtool: install: /usr/bin/install -c .libs/libModel.a /usr/local/
libtool: install: chmod 644 /usr/local/
libtool: install: ranlib /usr/local/
libtool: finish: PATH="/
-------
Libraries have been installed in:
/usr/local/lib
If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
- add LIBDIR to the `LD_LIBRARY_PATH' environment variable
during execution
- add LIBDIR to the `LD_RUN_PATH' environment variable
during linking
- use the `-Wl,-rpath -Wl,LIBDIR' linker flag
- have your system administrator add LIBDIR to `/etc/ld.so.conf'
See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
-------
make[2]: Für das Ziel »install-data-am« ist nichts zu tun.
make[2]: Leaving directory `/home/
make[1]: Leaving directory `/home/
Making install in Fields
make[1]: Entering directory `/home/
make[2]: Entering directory `/home/
/usr/bin/mkdir -p '/usr/local/lib'
/bin/sh ../libtool --mode=install /usr/bin/install -c libFields.la '/usr/local/lib'
libtool: install: warning: relinking `libFields.la'
libtool: install: (cd /home/djamil/
libtool: relink: mpic++ -fPIC -DPIC -shared -nostdlib /usr/lib64/
libtool: install: /usr/bin/install -c .libs/libFields
libtool: install: (cd /usr/local/lib && { ln -s -f libFields-2.3.so libFields.so || { rm -f libFields.so && ln -s libFields-2.3.so libFields.so; }; })
libtool: install: /usr/bin/install -c .libs/libFields.lai /usr/local/
libtool: install: /usr/bin/install -c .libs/libFields.a /usr/local/
libtool: install: chmod 644 /usr/local/
libtool: install: ranlib /usr/local/
libtool: finish: PATH="/
-------
Libraries have been installed in:
/usr/local/lib
If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
- add LIBDIR to the `LD_LIBRARY_PATH' environment variable
during execution
- add LIBDIR to the `LD_RUN_PATH' environment variable
during linking
- use the `-Wl,-rpath -Wl,LIBDIR' linker flag
- have your system administrator add LIBDIR to `/etc/ld.so.conf'
See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
-------
make[2]: Für das Ziel »install-data-am« ist nichts zu tun.
make[2]: Leaving directory `/home/
make[1]: Leaving directory `/home/
Making install in Parallel
make[1]: Entering directory `/home/
make[2]: Entering directory `/home/
/usr/bin/mkdir -p '/usr/local/lib'
/bin/sh ../libtool --mode=install /usr/bin/install -c libParallel.la '/usr/local/lib'
libtool: install: warning: relinking `libParallel.la'
libtool: install: (cd /home/djamil/
libtool: relink: mpic++ -fPIC -DPIC -shared -nostdlib /usr/lib64/
libtool: install: /usr/bin/install -c .libs/libParall
libtool: install: (cd /usr/local/lib && { ln -s -f libParallel.
libtool: install: (cd /usr/local/lib && { ln -s -f libParallel.
libtool: install: /usr/bin/install -c .libs/libParall
libtool: install: /usr/bin/install -c .libs/libParallel.a /usr/local/
libtool: install: chmod 644 /usr/local/
libtool: install: ranlib /usr/local/
libtool: finish: PATH="/
-------
Libraries have been installed in:
/usr/local/lib
If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
- add LIBDIR to the `LD_LIBRARY_PATH' environment variable
during execution
- add LIBDIR to the `LD_RUN_PATH' environment variable
during linking
- use the `-Wl,-rpath -Wl,LIBDIR' linker flag
- have your system administrator add LIBDIR to `/etc/ld.so.conf'
See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
-------
make[2]: Für das Ziel »install-data-am« ist nichts zu tun.
make[2]: Leaving directory `/home/
make[1]: Leaving directory `/home/
Making install in Tools
make[1]: Entering directory `/home/
Making install in dump2geo
make[2]: Entering directory `/home/
make[3]: Entering directory `/home/
/usr/bin/mkdir -p '/usr/local/bin'
/bin/sh ../../libtool --mode=install /usr/bin/install -c dump2geo '/usr/local/bin'
libtool: install: /usr/bin/install -c .libs/dump2geo /usr/local/
make[3]: Für das Ziel »install-data-am« ist nichts zu tun.
make[3]: Leaving directory `/home/
make[2]: Leaving directory `/home/
Making install in dump2pov
make[2]: Entering directory `/home/
make[3]: Entering directory `/home/
/usr/bin/mkdir -p '/usr/local/bin'
/bin/sh ../../libtool --mode=install /usr/bin/install -c dump2pov '/usr/local/bin'
libtool: install: /usr/bin/install -c .libs/dump2pov /usr/local/
make[3]: Für das Ziel »install-data-am« ist nichts zu tun.
make[3]: Leaving directory `/home/
make[2]: Leaving directory `/home/
Making install in mesh2pov
make[2]: Entering directory `/home/
make[3]: Entering directory `/home/
/usr/bin/mkdir -p '/usr/local/bin'
/bin/sh ../../libtool --mode=install /usr/bin/install -c mesh2pov '/usr/local/bin'
libtool: install: /usr/bin/install -c .libs/mesh2pov /usr/local/
make[3]: Für das Ziel »install-data-am« ist nichts zu tun.
make[3]: Leaving directory `/home/
make[2]: Leaving directory `/home/
Making install in rotextract
make[2]: Entering directory `/home/
make[3]: Entering directory `/home/
/usr/bin/mkdir -p '/usr/local/bin'
/bin/sh ../../libtool --mode=install /usr/bin/install -c rotextract '/usr/local/bin'
libtool: install: /usr/bin/install -c .libs/rotextract /usr/local/
make[3]: Für das Ziel »install-data-am« ist nichts zu tun.
make[3]: Leaving directory `/home/
make[2]: Leaving directory `/home/
Making install in StressCalculator
make[2]: Entering directory `/home/
make[3]: Entering directory `/home/
/usr/bin/mkdir -p '/usr/local/lib'
/bin/sh ../../libtool --mode=install /usr/bin/install -c libStressCalcul
libtool: install: warning: relinking `libStressCalcu
libtool: install: (cd /home/djamil/
libtool: relink: mpic++ -fPIC -DPIC -shared -nostdlib /usr/lib64/
libtool: install: /usr/bin/install -c .libs/libStress
libtool: install: (cd /usr/local/lib && { ln -s -f libStressCalcul
libtool: install: /usr/bin/install -c .libs/libStress
libtool: install: /usr/bin/install -c .libs/libStress
libtool: install: chmod 644 /usr/local/
libtool: install: ranlib /usr/local/
libtool: finish: PATH="/
-------
Libraries have been installed in:
/usr/local/lib
If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
- add LIBDIR to the `LD_LIBRARY_PATH' environment variable
during execution
- add LIBDIR to the `LD_RUN_PATH' environment variable
during linking
- use the `-Wl,-rpath -Wl,LIBDIR' linker flag
- have your system administrator add LIBDIR to `/etc/ld.so.conf'
See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
-------
/usr/bin/mkdir -p '/usr/local/bin'
/bin/sh ../../libtool --mode=install /usr/bin/install -c raw2tostress '/usr/local/bin'
libtool: install: /usr/bin/install -c .libs/raw2tostress /usr/local/
make[3]: Für das Ziel »install-data-am« ist nichts zu tun.
make[3]: Leaving directory `/home/
make[2]: Leaving directory `/home/
Making install in ExtractGrains
make[2]: Entering directory `/home/
make[3]: Entering directory `/home/
/usr/bin/mkdir -p '/usr/local/bin'
/bin/sh ../../libtool --mode=install /usr/bin/install -c grainextract '/usr/local/bin'
libtool: install: /usr/bin/install -c .libs/grainextract /usr/local/
make[3]: Für das Ziel »install-data-am« ist nichts zu tun.
make[3]: Leaving directory `/home/
make[2]: Leaving directory `/home/
Making install in dump2vtk
make[2]: Entering directory `/home/
make[3]: Entering directory `/home/
/usr/bin/mkdir -p '/usr/local/bin'
/bin/sh ../../libtool --mode=install /usr/bin/install -c dump2vtk '/usr/local/bin'
libtool: install: /usr/bin/install -c .libs/dump2vtk /usr/local/
make[3]: Für das Ziel »install-data-am« ist nichts zu tun.
make[3]: Leaving directory `/home/
make[2]: Leaving directory `/home/
Making install in ExtractFractures
make[2]: Entering directory `/home/
make[3]: Entering directory `/home/
/usr/bin/mkdir -p '/usr/local/bin'
/bin/sh ../../libtool --mode=install /usr/bin/install -c fracextract '/usr/local/bin'
libtool: install: /usr/bin/install -c .libs/fracextract /usr/local/
make[3]: Für das Ziel »install-data-am« ist nichts zu tun.
make[3]: Leaving directory `/home/
make[2]: Leaving directory `/home/
Making install in ForceChains
make[2]: Entering directory `/home/
make[3]: Entering directory `/home/
/usr/bin/mkdir -p '/usr/local/bin'
/bin/sh ../../libtool --mode=install /usr/bin/install -c fcconv '/usr/local/bin'
libtool: install: /usr/bin/install -c .libs/fcconv /usr/local/
make[3]: Für das Ziel »install-data-am« ist nichts zu tun.
make[3]: Leaving directory `/home/
make[2]: Leaving directory `/home/
Making install in ExtractStrain
make[2]: Entering directory `/home/
make[3]: Entering directory `/home/
/usr/bin/mkdir -p '/usr/local/bin'
/bin/sh ../../libtool --mode=install /usr/bin/install -c strainextract '/usr/local/bin'
libtool: install: /usr/bin/install -c .libs/strainextract /usr/local/
make[3]: Für das Ziel »install-data-am« ist nichts zu tun.
make[3]: Leaving directory `/home/
make[2]: Leaving directory `/home/
make[2]: Entering directory `/home/
make[3]: Entering directory `/home/
make[3]: Für das Ziel »install-exec-am« ist nichts zu tun.
make[3]: Für das Ziel »install-data-am« ist nichts zu tun.
make[3]: Leaving directory `/home/
make[2]: Leaving directory `/home/
make[1]: Leaving directory `/home/
Making install in Python
make[1]: Entering directory `/home/
Making install in MpiPython
make[2]: Entering directory `/home/
make[3]: Entering directory `/home/
/usr/bin/mkdir -p '/usr/local/bin'
/bin/sh ../../libtool --mode=install /usr/bin/install -c esysparticle '/usr/local/bin'
libtool: install: /usr/bin/install -c .libs/esysparticle /usr/local/
/usr/bin/mkdir -p '/usr/local/bin'
/usr/bin/install -c mpipython '/usr/local/bin'
make[3]: Für das Ziel »install-data-am« ist nichts zu tun.
make[3]: Leaving directory `/home/
make[2]: Leaving directory `/home/
Making install in BoostPythonUtil
make[2]: Entering directory `/home/
make[3]: Entering directory `/home/
/usr/bin/mkdir -p '/usr/local/lib'
/bin/sh ../../libtool --mode=install /usr/bin/install -c libBoostPythonU
libtool: install: /usr/bin/install -c .libs/libBoostP
libtool: install: (cd /usr/local/lib && { ln -s -f libBoostPythonU
libtool: install: /usr/bin/install -c .libs/libBoostP
libtool: install: /usr/bin/install -c .libs/libBoostP
libtool: install: chmod 644 /usr/local/
libtool: install: ranlib /usr/local/
libtool: finish: PATH="/
-------
Libraries have been installed in:
/usr/local/lib
If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
- add LIBDIR to the `LD_LIBRARY_PATH' environment variable
during execution
- add LIBDIR to the `LD_RUN_PATH' environment variable
during linking
- use the `-Wl,-rpath -Wl,LIBDIR' linker flag
- have your system administrator add LIBDIR to `/etc/ld.so.conf'
See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
-------
make[3]: Für das Ziel »install-data-am« ist nichts zu tun.
make[3]: Leaving directory `/home/
make[2]: Leaving directory `/home/
Making install in esys
make[2]: Entering directory `/home/
Making install in lsm
make[3]: Entering directory `/home/
Making install in util
make[4]: Entering directory `/home/
make[5]: Entering directory `/home/
make[5]: Für das Ziel »install-exec-am« ist nichts zu tun.
/usr/bin/mkdir -p '/usr/local/
/usr/bin/install -c -m 644 __init__.py FileUtil.py OptParse.py pathSearcher.py process.py '/usr/local/
Byte-compiling python modules...
__init_
Byte-compiling python modules (optimized versions) ...
__init_
/usr/bin/mkdir -p '/usr/local/
/bin/sh ../../../../libtool --mode=install /usr/bin/install -c libFoundationPy.la FoundationPy.la '/usr/local/
libtool: install: warning: relinking `libFoundationP
libtool: install: (cd /home/djamil/
libtool: relink: mpic++ -fPIC -DPIC -shared -nostdlib /usr/lib64/
libtool: install: /usr/bin/install -c .libs/libFounda
libtool: install: (cd /usr/local/
libtool: install: (cd /usr/local/
libtool: install: /usr/bin/install -c .libs/libFounda
libtool: install: warning: relinking `FoundationPy.la'
libtool: install: (cd /home/djamil/
libtool: relink: mpic++ -fPIC -DPIC -shared -nostdlib /usr/lib64/
libtool: install: /usr/bin/install -c .libs/Foundatio
libtool: install: (cd /usr/local/
libtool: install: (cd /usr/local/
libtool: install: /usr/bin/install -c .libs/Foundatio
libtool: finish: PATH="/
-------
Libraries have been installed in:
/usr/
If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
- add LIBDIR to the `LD_LIBRARY_PATH' environment variable
during execution
- add LIBDIR to the `LD_RUN_PATH' environment variable
during linking
- use the `-Wl,-rpath -Wl,LIBDIR' linker flag
- have your system administrator add LIBDIR to `/etc/ld.so.conf'
See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
-------
/usr/bin/python -c 'from __future__ import print_function;\
import os;\
writefile=
readfile=
text=
(\
"
"
"
"2.3",\
"https:/
"
"no",\
"False",\
"False"\
);\
print(
readfile.
writefile.
'
/usr/bin/mkdir -p '/usr/local/
/usr/bin/install -c -m 644 InstallInfo.py '/usr/local/
Byte-compiling python modules...
InstallInfo.py
Byte-compiling python modules (optimized versions) ...
InstallInfo.py
make[5]: Leaving directory `/home/
make[4]: Leaving directory `/home/
Making install in .
make[4]: Entering directory `/home/
make[5]: Entering directory `/home/
make[5]: Für das Ziel »install-exec-am« ist nichts zu tun.
/usr/bin/mkdir -p '/usr/local/
/bin/sh ../../../libtool --mode=install /usr/bin/install -c libLsmPy.la LsmPy.la '/usr/local/
libtool: install: warning: relinking `libLsmPy.la'
libtool: install: (cd /home/djamil/
libtool: relink: mpic++ -fPIC -DPIC -shared -nostdlib /usr/lib64/
libtool: install: /usr/bin/install -c .libs/libLsmPy.
libtool: install: (cd /usr/local/
libtool: install: (cd /usr/local/
libtool: install: /usr/bin/install -c .libs/libLsmPy.lai /usr/local/
libtool: install: warning: relinking `LsmPy.la'
libtool: install: (cd /home/djamil/
libtool: relink: mpic++ -fPIC -DPIC -shared -nostdlib /usr/lib64/
libtool: install: /usr/bin/install -c .libs/LsmPy.
libtool: install: (cd /usr/local/
libtool: install: (cd /usr/local/
libtool: install: /usr/bin/install -c .libs/LsmPy.lai /usr/local/
libtool: finish: PATH="/
-------
Libraries have been installed in:
/usr/
If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
- add LIBDIR to the `LD_LIBRARY_PATH' environment variable
during execution
- add LIBDIR to the `LD_RUN_PATH' environment variable
during linking
- use the `-Wl,-rpath -Wl,LIBDIR' linker flag
- have your system administrator add LIBDIR to `/etc/ld.so.conf'
See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
-------
/usr/bin/mkdir -p '/usr/local/
/usr/bin/install -c -m 644 __init__.py Logging.py '/usr/local/
Byte-compiling python modules...
__init_
Byte-compiling python modules (optimized versions) ...
__init_
make[5]: Leaving directory `/home/
make[4]: Leaving directory `/home/
Making install in geometry
make[4]: Entering directory `/home/
make[5]: Entering directory `/home/
make[5]: Für das Ziel »install-exec-am« ist nichts zu tun.
/usr/bin/mkdir -p '/usr/local/
/bin/sh ../../../../libtool --mode=install /usr/bin/install -c libGeometryPy.la GeometryPy.la '/usr/local/
libtool: install: warning: relinking `libGeometryPy.la'
libtool: install: (cd /home/djamil/
libtool: relink: mpic++ -fPIC -DPIC -shared -nostdlib /usr/lib64/
libtool: install: /usr/bin/install -c .libs/libGeomet
libtool: install: (cd /usr/local/
libtool: install: (cd /usr/local/
libtool: install: /usr/bin/install -c .libs/libGeomet
libtool: install: warning: relinking `GeometryPy.la'
libtool: install: (cd /home/djamil/
libtool: relink: mpic++ -fPIC -DPIC -shared -nostdlib /usr/lib64/
libtool: install: /usr/bin/install -c .libs/GeometryP
libtool: install: (cd /usr/local/
libtool: install: (cd /usr/local/
libtool: install: /usr/bin/install -c .libs/GeometryP
libtool: finish: PATH="/
-------
Libraries have been installed in:
/usr/
If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
- add LIBDIR to the `LD_LIBRARY_PATH' environment variable
during execution
- add LIBDIR to the `LD_RUN_PATH' environment variable
during linking
- use the `-Wl,-rpath -Wl,LIBDIR' linker flag
- have your system administrator add LIBDIR to `/etc/ld.so.conf'
See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
-------
/usr/bin/mkdir -p '/usr/local/
/usr/bin/install -c -m 644 __init__.py SingleParticleG
Byte-compiling python modules...
__init_
Byte-compiling python modules (optimized versions) ...
__init_
make[5]: Leaving directory `/home/
make[4]: Leaving directory `/home/
Making install in vis
make[4]: Entering directory `/home/
Making install in core
make[5]: Entering directory `/home/
make[6]: Entering directory `/home/
make[6]: Für das Ziel »install-exec-am« ist nichts zu tun.
/usr/bin/mkdir -p '/usr/local/
/usr/bin/install -c -m 644 __init__.py arrow.py arrowExtractor.py box.py camera.py capsule.py color.py cone.py cylinder.py cylinderExtract
Byte-compiling python modules...
__init_
Byte-compiling python modules (optimized versions) ...
__init_
make[6]: Leaving directory `/home/
make[5]: Leaving directory `/home/
make[5]: Entering directory `/home/
make[6]: Entering directory `/home/
make[6]: Für das Ziel »install-exec-am« ist nichts zu tun.
/usr/bin/mkdir -p '/usr/local/
/usr/bin/install -c -m 644 __init__.py '/usr/local/
Byte-compiling python modules...
__init__.py
Byte-compiling python modules (optimized versions) ...
__init__.py
make[6]: Leaving directory `/home/
make[5]: Leaving directory `/home/
make[4]: Leaving directory `/home/
make[3]: Leaving directory `/home/
make[3]: Entering directory `/home/
make[4]: Entering directory `/home/
make[4]: Für das Ziel »install-exec-am« ist nichts zu tun.
/usr/bin/mkdir -p '/usr/local/
/usr/bin/install -c -m 644 __init__.py '/usr/local/
Byte-compiling python modules...
__init__.py
Byte-compiling python modules (optimized versions) ...
__init__.py
make[4]: Leaving directory `/home/
make[3]: Leaving directory `/home/
make[2]: Leaving directory `/home/
Making install in epydoc
make[2]: Entering directory `/home/
Making install in .
make[3]: Entering directory `/home/
make[4]: Entering directory `/home/
make install-exec-hook
make[5]: Entering directory `/home/
make[5]: Für das Ziel »install-exec-hook« ist nichts zu tun.
make[5]: Leaving directory `/home/
make[4]: Für das Ziel »install-data-am« ist nichts zu tun.
make[4]: Leaving directory `/home/
make[3]: Leaving directory `/home/
make[2]: Leaving directory `/home/
Making install in .
make[2]: Entering directory `/home/
make[3]: Entering directory `/home/
make install-exec-hook
make[4]: Entering directory `/home/
make[4]: Für das Ziel »install-exec-hook« ist nichts zu tun.
make[4]: Leaving directory `/home/
make[3]: Für das Ziel »install-data-am« ist nichts zu tun.
make[3]: Leaving directory `/home/
make[2]: Leaving directory `/home/
make[1]: Leaving directory `/home/
Making install in Doc/Tutorial
make[1]: Entering directory `/home/
make[2]: Entering directory `/home/
make[2]: Für das Ziel »install-exec-am« ist nichts zu tun.
/usr/bin/mkdir -p '/usr/local/
/usr/bin/install -c -m 644 ./../ESyS-
make[2]: Leaving directory `/home/
make[1]: Leaving directory `/home/
make[1]: Entering directory `/home/
make[2]: Entering directory `/home/
make[2]: Für das Ziel »install-exec-am« ist nichts zu tun.
make[2]: Für das Ziel »install-data-am« ist nichts zu tun.
make[2]: Leaving directory `/home/
make[1]: Leaving directory `/home/
Thanks so much!
Revision history for this message
|
#15 |
Hello Djamil.
I get the impression that there is (among other things) a path issue here. When attempting to install as djamil, "make" reports that mpic++ cannot be found. When installing as root, "make" has no such problem. Then, after "make install" as root, even though you can see installation files under /usr/local/
You can also try installing under your home folder rather thanunder /usr/local/ (replacing "installs/esys-p" with whatever you like):
[sudo] make uninstall
make distclean
export PATH=$HOME/
export LD_LIBRARY_
export LIBRARY_
export PYTHONPATH=
./configure CC=mpicc CXX=mpic++ --prefix=
make
make install
I have no idea how useful this change will be, but I hope that it can eliminate at least one of the problems that have been occurring.
One last thing: Perhaps the problem is missing packages and not path. If you installed OpenMPI from packages, check that you have the development files installed as well as any runtime files. I don't know how they are named for Fedora; under Debian the development package is libopenmpi-dev and the main package is openmpi-bin.
Vince
Revision history for this message
|
#16 |
Thanks a lot Vince, this worked! I knew about the Path issues and I followed all the suggestions in the Forum, still I'm unsure what the problem was, as actually typing mpicc or mpic++ in the command worked although make didn't seem to find it.
Anyway, installing ESyS in the directory you proposed everything now seems to work fine!
I want to thank all of you very much for your help!
Djamil
Revision history for this message
|
#17 |
Hi Djamil.
I'm glad that you worked around the problem. Perhaps Fedora requires another path setting for installations needing root access. If at some time you discover how to resolve the issue, please tell the ESyS-Particle user community. In the meantime, I hope that you find the code helpful.
Regards,
Vince
Revision history for this message
|
#18 |
Hello,
This solution has been very useful.
Just a follow up question. Can you append these new paths to the bashrc the same way? I tried adding them to my bashrc file but it does not seem to work.
Thank you.
Regards,
Kahlil Cui
Revision history for this message
|
#19 |
Hi Kahlil,
Yes, it should be possible to add the new paths to bashrc. Not sure why it did not work for you.
A couple of possibilities:
1) after editting bashrc, might need to logout of the terminal and open a new terminal for the changes to take effect,
2) perhaps you are not using bash as your default shell environment?
To find out the default shell on your system, run this command:
echo $SHELL
To find out which shell you are currently using, run this command from the terminal:
echo $0
If these return 'bash' then your bashrc should be executed upon opening a terminal or bash shell.
Please post the last ten lines or so of your bashrc file, if you continue to have problems.
Cheers,
Dion
Revision history for this message
|
#20 |
Hello!
Thank you very much for your reply. I have tried what you instructed and all of them returned bash.The last lines of my bashrc file are the ff:
export PATH=$HOME/
export LD_LIBRARY_
export LIBRARY_
export PYTHONPATH=
export PATH=/yourPovra
export PATH=/usr/
export LD_LIBRARY_
export LIBRARY_
export PYTHONPATH=
export PATH=/usr/
alias of231='source $HOME/OpenFOAM/
alias of231='source $HOME/OpenFOAM/
# added by Anaconda2 installer
export PATH="/
I manually inputted the paths of the home folder and I also kept the paths of the usr/local. I tested it using bingle.py but it won't work unless I manually enter the paths.
Hoping for your ideas on this.
Respectfully,
Kahlil Cui
Revision history for this message
|
#21 |
Hi Kahlil,
Try moving the $HOME export commands to the very end of the bashrc file.
Also add the following line after the export commands:
echo "Hi there Kahlil!"
Once you save the bashrc file, open a new terminal window. Hopefully you will see the welcome message in that terminal. If not, we have a problem: your bashrc is not being read when shells open.
If you see the welcome message, try the bingle.py test again.
Also, check that $HOME/installs/
Cheers,
Dion
Revision history for this message
|
#22 |
Hello Dion,
It is working now. Thank you very much! The solution was so simple. I am very new to linux and bash files and such solutions are really unfamiliar to me.
Thank you once again!
Respectfully,
Kahlil Cui
Revision history for this message
|
#23 |
No worries Kahlil. Welcome to linux!
Do some reading on "shell environment variables" to learn a bit more about bash and how it works.
Cheers,
Dion