Unicorn

unable to install dolfin-0.8.2-hpc

Asked by algra

I would like to install Unicorn 0.1.3-hpc. For that, I installed the required old versions of ufc and ffc as stated in README. I am also trying to install dolfin-0.8.2-hpc with the same purpose, however when I complile I get the error:

alba@feo:~/src/dolfin-0.8.2-hpc$ make
Making all in src
make[1]: Entering directory `/home/alba/src/dolfin-0.8.2-hpc/src'
Making all in common
make[2]: Entering directory `/home/alba/src/dolfin-0.8.2-hpc/src/common'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/home/alba/src/dolfin-0.8.2-hpc/src/common'
Making all in elements
make[2]: Entering directory `/home/alba/src/dolfin-0.8.2-hpc/src/elements'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/home/alba/src/dolfin-0.8.2-hpc/src/elements'
Making all in fem
make[2]: Entering directory `/home/alba/src/dolfin-0.8.2-hpc/src/fem'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/home/alba/src/dolfin-0.8.2-hpc/src/fem'
Making all in function
make[2]: Entering directory `/home/alba/src/dolfin-0.8.2-hpc/src/function'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/home/alba/src/dolfin-0.8.2-hpc/src/function'
Making all in graph
make[2]: Entering directory `/home/alba/src/dolfin-0.8.2-hpc/src/graph'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/home/alba/src/dolfin-0.8.2-hpc/src/graph'
Making all in io
make[2]: Entering directory `/home/alba/src/dolfin-0.8.2-hpc/src/io'
/bin/bash ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../include/dolfin/config -I/usr/include/libxml2 -I../../include -I/usr/local/include -g -O2 -MT MFile.lo -MD -MP -MF .deps/MFile.Tpo -c -o MFile.lo MFile.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../include/dolfin/config -I/usr/include/libxml2 -I../../include -I/usr/local/include -g -O2 -MT MFile.lo -MD -MP -MF .deps/MFile.Tpo -c MFile.cpp -o MFile.o
MFile.cpp: In member function 'virtual void dolfin::MFile::operator<<(dolfin::GenericVector&)':
MFile.cpp:38:41: error: 'fopen' was not declared in this scope
MFile.cpp:41:22: error: 'fprintf' was not declared in this scope
MFile.cpp:53:12: error: 'fclose' was not declared in this scope
MFile.cpp: In member function 'virtual void dolfin::MFile::operator<<(dolfin::Mesh&)':
MFile.cpp:63:41: error: 'fopen' was not declared in this scope
MFile.cpp:68:34: error: 'fprintf' was not declared in this scope
MFile.cpp:86:28: error: 'fprintf' was not declared in this scope
MFile.cpp:88:45: error: 'fprintf' was not declared in this scope
MFile.cpp:97:52: error: 'fprintf' was not declared in this scope
MFile.cpp:99:50: error: 'fprintf' was not declared in this scope
MFile.cpp:103:65: error: 'fprintf' was not declared in this scope
MFile.cpp:105:62: error: 'fprintf' was not declared in this scope
MFile.cpp:108:18: error: 'fprintf' was not declared in this scope
MFile.cpp:135:12: error: 'fclose' was not declared in this scope
make[2]: *** [MFile.lo] Error 1
make[2]: Leaving directory `/home/alba/src/dolfin-0.8.2-hpc/src/io'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/alba/src/dolfin-0.8.2-hpc/src'
make: *** [all-recursive] Error 1

I believe this is not related to the message I got when installing ufc:

alba@feo:~/src/ufc-1.1.1$ sudo scons install
[sudo] password for alba:
scons: Reading SConscript files ...

scons: warning: The PathOption() function is deprecated; use the PathVariable() function instead.
File "/home/alba/src/ufc-1.1.1/SConstruct", line 34, in <module>

scons: warning: The BoolOption() function is deprecated; use the BoolVariable() function instead.
File "/home/alba/src/ufc-1.1.1/SConstruct", line 39, in <module>

scons: warning: The Options class is deprecated; use the Variables class instead.
File "/home/alba/src/ufc-1.1.1/SConstruct", line 53, in <module>
Checking for SWIG...(cached) yes
Checking for SWIG version > 1.3.35...(cached) yes
Checking for Boost...(cached) yes
Checking for Python...(cached) yes
scons: done reading SConscript files.
scons: Building targets ...
scons: `install' is up to date.
scons: done building targets.

---------------------------------------------------------
*** Warning: Old ufc module

    /usr/lib/python2.7/dist-packages/ufc

still excists in installation path.
Try remove these files with:

    scons -c cleanOldUFC=Yes

Note that you may need to be root.

What am I doing wrong?

Many thanks.

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Revision history for this message
Aurélien Larcher (aurelien-larcher) said : 		#1

You just need to add an include for stdio.h in MFile.cpp.
I believe it is fixed in 0.8.3-hpc.
Cheers

Aurelien

Revision history for this message
Niclas Jansson (njansson) said : 		#2

Aurélien Larcher <email address hidden> writes:

> Question #229345 on Unicorn changed:
> https://answers.launchpad.net/unicorn/+question/229345
>
> Status: Open => Answered
>
> Aurélien Larcher proposed the following answer:
> You just need to add an include for stdio.h in MFile.cpp.
> I believe it is fixed in 0.8.3-hpc.
> Cheers
>
> Aurelien

Yes, these and several other bug fixes has been fixed in 0.8.3-hpc,
which can be downloaded from dryad.csc.kth.se

Cheers,
Niclas

Revision history for this message
algra (algra) said : 		#3

Many thanks for your quick responses. However I must stick to Dolfin-0.8.2-hpc (and not to later versions) to install and run Unicorn-0.1.3-hpc, right?

Revision history for this message
Niclas Jansson (njansson) said : 		#4

algra <email address hidden> writes:

> Question #229345 on Unicorn changed:
> https://answers.launchpad.net/unicorn/+question/229345
>
> algra posted a new comment:
> Many thanks for your quick responses. However I must stick to
> Dolfin-0.8.2-hpc (and not to later versions) to install and run
> Unicorn-0.1.3-hpc, right?

No, Unicorn 0.1.3-hpc will work fine together with DOLFIN
0.8.3-hpc. However, you need to patch the configure.ac file of Unicorn
such that it will accept the newer DOLFIN version, i.e.,

Change,

PKG_CHECK_MODULES([DOLFIN], [dolfin = 0.8.2-hpc])

to,

PKG_CHECK_MODULES([DOLFIN], [dolfin = 0.8.3-hpc])

and don't forget to run regen.sh before reconfigure Unicorn.

Niclas

PS. We will release a new version of Unicorn soon (available from
dryad.csc.kth.se)

Revision history for this message
algra (algra) said : 		#5

I see, thank you very much for the detailed answer; that's really appreciated.

Unfortunately, I get error messages when installing dolfin-0.8.3-hpc:

checking for inflateEnd in -lz... yes
configure: error: Linear Algebra backend not found

As Ji Peng in #4 (https://answers.launchpad.net/unicorn/+question/224407) suggested, I installed the version 2.3.3 of PETSc. I get exactly the same message. My excuses for this question-bombing, but would anyone know how this could be solved?

Thank you very much.

Revision history for this message
algra (algra) said : 		#6

Sorry, I forgot to say that I gave the argument --with-petsc to ./configure, but no success:

checking for PETSc... no
configure: error: Linear Algebra backend not found

Revision history for this message
Niclas Jansson (njansson) said : 		#7

algra <email address hidden> writes:

> Question #229345 on Unicorn changed:
> https://answers.launchpad.net/unicorn/+question/229345
>
> algra posted a new comment:
> Sorry, I forgot to say that I gave the argument --with-petsc to
> ./configure, but no success:
>
> checking for PETSc... no
> configure: error: Linear Algebra backend not found

Try to give the configure script the hint, --with-petsc-dir= which
should point to the PETSc directory.

Niclas

Revision history for this message
algra (algra) said : 		#8

Thank you, Niclas. Since apparently I have petsc installed in two different directories:

alba@feo:~/src/dolfin-0.8.3-hpc$ whereis petsc
petsc: /usr/lib/petsc /usr/include/petsc

i have tried --with-petsc-dir=/usr/include/petsc , with no success. However, I have download petsc-2.3.3 in ~/src/petsc-2.3.3-p16, and I successfully configured and compiled dolfin. I further configured unicorn with no errors, but when I compile I get errors with MPI_comm:

AdaptiveRefinement.cpp:281:3: error: invalid conversion from 'int' to 'MPI_Comm {aka ompi_communicator_t*}' [-fpermissive]
/usr/lib/openmpi/include/mpi.h:874:20: error: initializing argument 6 of 'int MPI_Allreduce(void*, void*, int, MPI_Datatype, MPI_Op, MPI_Comm)' [-fpermissive]
AdaptiveRefinement.cpp:298:29: error: invalid conversion from 'int' to 'MPI_Comm {aka ompi_communicator_t*}' [-fpermissive]
/usr/lib/openmpi/include/mpi.h:1208:20: error: initializing argument 11 of 'int MPI_Sendrecv(void*, int, MPI_Datatype, int, int, void*, int, MPI_Datatype, int, int, MPI_Comm, MPI_Status*)' [-fpermissive]
AdaptiveRefinement.cpp:302:51: error: invalid conversion from 'int' to 'MPI_Comm {aka ompi_communicator_t*}' [-fpermissive]
/usr/lib/openmpi/include/mpi.h:1208:20: error: initializing argument 11 of 'int MPI_Sendrecv(void*, int, MPI_Datatype, int, int, void*, int, MPI_Datatype, int, int, MPI_Comm, MPI_Status*)' [-fpermissive]
make[1]: *** [AdaptiveRefinement.lo] Error 1
make[1]: Leaving directory `/home/alba/src/unicorn-0.1.3-hpc/src'
make: *** [all-recursive] Error 1

Could it be related to the new location of petsc? My apologies for all these questions...

Revision history for this message
Thomas Ward (thomas-ward) said : 		#9

Hi Algra,

...probably too late for you but someone else might benefit...

with
dolfin-hpc.0.8.4

./configure --with-petsc --with-petsc-dir=/usr/lib/petsc

worked for me on Ubuntu 14.04 without having to compile a new petsc

did you manage to get unicorn 1.3 working on Ubuntu in the end?

regards

Thomas

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