Can't install the esys-particle

Asked by Wasin Meesuay on 2020-09-24

Hi

I tried to install esys-particle through the Ubuntu Bash on Window10.
The problem start since I type

>> sh autogen.sh

and the bash respond as

Model/Makefile.am:26: warning: source file '$(top_srcdir)/Fields/FieldMaster.cpp' is in a subdirectory,
Model/Makefile.am:26: but option 'subdir-objects' is disabled
automake: warning: possible forward-incompatibility.
automake: At least a source file is in a subdirectory, but the 'subdir-objects'
automake: automake option hasn't been enabled. For now, the corresponding output
automake: object file(s) will be placed in the top-level directory. However,
automake: this behaviour will change in future Automake versions: they will
automake: unconditionally cause object files to be placed in the same subdirectory
automake: of the corresponding sources.
automake: You are advised to start using 'subdir-objects' option throughout your
automake: project, to avoid future incompatibilities.
Model/Makefile.am:26: warning: source file '$(top_srcdir)/Fields/FieldSlave.cpp' is in a subdirectory,
Model/Makefile.am:26: but option 'subdir-objects' is disabled
Model/Makefile.am:26: warning: source file '$(top_srcdir)/Fields/WallFieldMaster.cpp' is in a subdirectory,
Model/Makefile.am:26: but option 'subdir-objects' is disabled
Model/Makefile.am:26: warning: source file '$(top_srcdir)/Fields/WallFieldSlave.cpp' is in a subdirectory,
Model/Makefile.am:26: but option 'subdir-objects' is disabled
Model/Makefile.am:26: warning: source file '$(top_srcdir)/Parallel/CheckPointable.cpp' is in a subdirectory,
Model/Makefile.am:26: but option 'subdir-objects' is disabled
Model/Makefile.am:26: warning: source file '$(top_srcdir)/Parallel/Mesh2DReader.cpp' is in a subdirectory,
Model/Makefile.am:26: but option 'subdir-objects' is disabled
Model/Makefile.am:26: warning: source file '$(top_srcdir)/Parallel/Mesh2DReaderImpl.cpp' is in a subdirectory,
Model/Makefile.am:26: but option 'subdir-objects' is disabled
Model/Makefile.am:26: warning: source file '$(top_srcdir)/Parallel/MeshReader.cpp' is in a subdirectory,
Model/Makefile.am:26: but option 'subdir-objects' is disabled
Model/Makefile.am:26: warning: source file '$(top_srcdir)/Parallel/MeshReaderImpl.cpp' is in a subdirectory,
Model/Makefile.am:26: but option 'subdir-objects' is disabled
Model/Makefile.am:26: warning: source file '$(top_srcdir)/Parallel/vec3_mpi.cpp' is in a subdirectory,
Model/Makefile.am:26: but option 'subdir-objects' is disabled
Parallel/Makefile.am:88: warning: whitespace following trailing backslash
revision-id: <email address hidden>
date: 2020-09-14 11:48:44 +0200
build-date: 2020-09-24 17:26:17 +0700
revno: 1217
branch-nick: trunk
bzr version header generated

how can I fix this??

Thank you for an advance,
Wasin

Question information

Language:
English Edit question
Status:
Solved
For:
ESyS-Particle Edit question
Assignee:
No assignee Edit question
Solved by:
Dion Weatherley
Solved:
2020-09-29
Last query:
2020-09-29
Last reply:
2020-09-29
Dion Weatherley (d-weatherley) said : #1

Hi Wasin,

These are all warning messages only. The autogen.sh script has completed execution and it is safe to continue to the next steps of building ESyS-Particle:
./configure CC=mpicc CXX=mpic++
make
sudo make install

For general information, the developers are currently testing a new build system based on cmake that will eventually replace automake. Consequently, we are unlikely to fix the problems leading to the warnings above.

Cheers,

Dion

Wasin Meesuay (kakkunno) said : #2

Dear Dion,

Thank you for your advice. But after I move on to

./configure CC=mpicc CXX=mpic++

the Ubuntu bash just respond

no...
no
configure: error: cannot find the flags to link with Boost python

and after I tried to move on to

make

 the bash respond as

make: *** No targets specified and no makefile found. Stop.

and can't do anything further (sudo make install).

*I download and install the python already.

Thank you in advance from thai student(_^_/||\_^_)

Wasin Meesuay (kakkunno) said : #3

Here is the whole respond of

./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... python3
checking for python3... /usr/bin/python3
checking for python3 version... 3.8
checking for the Python ABI tags...
checking for the location of the Python executable python3.8... /usr/local/bin/python3.8
checking for python3 platform... linux
checking for python3 script directory... ${prefix}/lib/python3/dist-packages
checking for python3 extension module directory... ${exec_prefix}/lib/python3/dist-packages
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking how to print strings... printf
checking whether make supports the include directive... yes (GNU style)
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 whether mpicc understands -c and -o together... yes
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 how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop
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 a working dd... /usr/bin/dd
checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1
checking for mt... mt
checking if mt 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... /usr/local/bin/povray
configure: POV-Ray support enabled
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 whether mpicc understands -c and -o together... (cached) yes
checking dependency style of mpicc... (cached) gcc3
checking how to run the C preprocessor... mpicc -E
checking for flex... flex
checking lex output file root... lex.yy
checking lex library... none needed
checking whether yytext is a pointer... no
checking for bison... bison -y
checking whether ln -s works... yes
checking for find... find
checking for laminfo... no
checking if CXX is mpic++ or mpiCC... mpic++
checking for Py_Main in -lpython3.8... yes
checking for Boost headers version >= 1.47.0... yes
checking for Boost's header version... 107100
Boost Version is 1.71.0
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/error_code.hpp usability... yes
checking boost/system/error_code.hpp presence... yes
checking for boost/system/error_code.hpp... yes
checking for the Boost system library... /usr/lib/x86_64-linux-gnu/libboost_system.so ...
libboost_system.so links to libboost_system.so.1.71.0
yes...
yes
checking boost/filesystem/path.hpp usability... yes
checking boost/filesystem/path.hpp presence... yes
checking for boost/filesystem/path.hpp... yes
checking for the Boost filesystem library... /usr/lib/x86_64-linux-gnu/libboost_filesystem.so ...
libboost_filesystem.so links to libboost_filesystem.so.1.71.0
yes...
(cached) 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... /usr/lib/x86_64-linux-gnu/libboost_python.so ...
no...
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configure: error: cannot find the flags to link with Boost python

Dion Weatherley (d-weatherley) said : #4

Hi Wasin,

Have you been following these instructions?
https://answers.launchpad.net/esys-particle/+faq/1613

In particular, have you installed all the mandatory dependencies?
> sudo apt-get install libtool automake build-essential bzr
> sudo apt-get install mpi-default-bin mpi-default-dev libboost-all-dev

The error messages you posted suggest you have not installed libboost-all-dev. ESyS-Particle requires openMPI (or mpich2) and a number of the boost libraries (libboost-filesystem, libboost-system, libboost-python and libboost-regex), in addition to python.

Cheers,

Dion

Wasin Meesuay (kakkunno) said : #5

Dear Dion,

I followed all the instruction from FAQ#1613, but the results still be the same. (T^T)

Manfred Hampl (m-hampl) said : #6

What is the output of the command

sudo apt install libboost-all-dev

Wasin Meesuay (kakkunno) said : #7

Dear Manfred,

Here is the output

Reading package lists... Done
Building dependency tree
Reading state information... Done
libboost-all-dev is already the newest version (1.71.0.0ubuntu2).
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

Manfred Hampl (m-hampl) said : #8

Probably a known problem, Bug #1865209

/usr/lib/x86_64-linux-gnu/libboost_python3-py38.so exists (as link) only in libboost-all-dev from boost 1.67, but not in libboost-all-dev from boost 1.71.

Eventually creating a link with target /usr/lib/x86_64-linux-gnu/libboost_python38.so helps.

Dion Weatherley (d-weatherley) said : #9

Thanks Manfred.

Wasin, I was able to reproduce your problem on a fresh ubuntu-20.04 installation. As Manfred said, it's a problem with libboost_python_1.71. Try this:

sudo ln -s /usr/lib/x86_64-linux-gnu/libboost_python38.so.1.71.0 /usr/lib/x86_64-linux-gnu/libboost_python3.so

then re-run configure:

./configure CC=mpicc CXX=mpic++

If that doesn't work, you may have a version of python2.7 on your system. You will need to remove all python2 packages. To check if these are installed:

dpkg -l |grep python2

Use "sudo apt remove ..." to remove these packages and then re-run configure again.

If the ./configure script gets past the libboost_python checks, you should be fine to continue with the installation procedure.

Wasin Meesuay (kakkunno) said : #10

Thank you all of you, Dion and Manfred,

I can go through until the final part and there is still something wrong after I tried to run

> mpirun -np 2 esysparticle bingle_output.py

and here is the output

esysparticle: error while loading shared libraries: libFoundation-2.3.5.so: cannot open shared object file: No such file or directory
esysparticle: error while loading shared libraries: libFoundation-2.3.5.so: cannot open shared object file: No such file or directory
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------

How can I fix this??

Regards,
Wasin

Hi Wasin,

Looks like you made it to the final step. Your PYTHONPATH is probably incorrect for a Python3 installation. Try the following command:

export PYTHONPATH=/usr/local/lib/python3/dist-packages/:$PYTHONPATH

then re-run the test simulation.

Cheers,

Dion

Wasin Meesuay (kakkunno) said : #12

Dear Dion,

it respond with this instead

CSubLatticeControler::initMPI()
python3: can't open file 'bingle_output.py': [Errno 2] No such file or directory

Regards,
Wasin

Hi Wasin,

Now is the time to start working through the ESyS-Particle Tutorial:
https://launchpad.net/esys-particle/2.3/2.3.1/+download/ESyS-Particle_Tutorial.pdf

bingle_output.py is one of the first simulation scripts discussed in the Tutorial. You will need to write a text file containing this script before testing ESyS-Particle on your computer.

Please note that the Tutorial is yet to be updated for python3. For the most part, you will simply need to change print statements to python3 syntax; by adding round brackets surrounding the information to write to the terminal.

Cheers,

Dion

Wasin Meesuay (kakkunno) said : #14

Thanks Dion Weatherley, that solved my question.