abinit 7.2.1 with openmpi

option, parallelism,...

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abinitfonda
Posts: 3
Joined: Sun May 19, 2013 12:41 pm

abinit 7.2.1 with openmpi

Post by abinitfonda » Sun May 19, 2013 1:47 pm

My installation procedure is following:
1. download plugins into ~/.abnint/tarballs
2. eneter folder abinit-7.2.1/builder/

Code: Select all

../configure  --with-mpi-prefix=/home/soft/mpi/openmpi-142-intel/    FC=mpif90


Code: Select all

make


Then problem appears:

checking for dummy main to link with Fortran libraries... none
checking for Fortran name-mangling scheme... lower case, underscore, no extra underscore
checking whether the compiler accepts very long lines... yes
checking whether the compiler accepts "line-number" lines cast by the preprocessor... yes
checking fortran 90 modules extension... mod
checking for the size of a Fortran integer... configure: error: in `/home/soft/abinit-7.2.1/builder/fallbacks/sources/libxc-2.0.1':
configure: error: f90 program to find the size of a Fortran integer failed
See `config.log' for more details
make[3]: *** [stamps/libxc-config-stamp] Error 1
make[3]: Leaving directory `/home/soft/abinit-7.2.1/builder/fallbacks'
make[2]: [all-local] Error 2 (ignored)
Checking build of libxc fallback
test -e stamps/libxc-install-stamp
make[2]: *** [all-local] Error 1
make[2]: Leaving directory `/home/soft/abinit-7.2.1/builder/fallbacks'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/soft/abinit-7.2.1/builder'
make: *** [all] Error 2


My config.log is attached, please give me a hand what's going wrong. Thanks!
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gmatteo
Posts: 291
Joined: Sun Aug 16, 2009 5:40 pm

Re: abinit 7.2.1 with openmpi

Post by gmatteo » Mon May 20, 2013 2:00 pm

The configuration of abinit completed successfully, the problem shows up during the configuration of libxc
We need the config.log file produced in /home/soft/abinit-7.2.1/builder/fallbacks/sources/libxc-2.0.1

BTW:
Your version of gcc (C- compiler) is pretty old:

gcc (GCC) 4.1.2 20070115 (SUSE Linux)

I don't know if this is the reason of the error, but I would suggest using a more recent version of GCC
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abinitfonda
Posts: 3
Joined: Sun May 19, 2013 12:41 pm

Re: abinit 7.2.1 with openmpi

Post by abinitfonda » Sun May 26, 2013 10:35 am

gmatteo wrote:The configuration of abinit completed successfully, the problem shows up during the configuration of libxc
We need the config.log file produced in /home/soft/abinit-7.2.1/builder/fallbacks/sources/libxc-2.0.1

BTW:
Your version of gcc (C- compiler) is pretty old:

gcc (GCC) 4.1.2 20070115 (SUSE Linux)

I don't know if this is the reason of the error, but I would suggest using a more recent version of GCC


Thanks, gmatteo!

After I substituted it with a newer version (gcc (GCC) 4.6.4), problem still exists. Could you please help me
have a look at the config.log file (from /home/soft/abinit-7.2.1/builder/fallbacks/sources/libxc-2.0.1) as you asked?

Thanks again!

Ted
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gmatteo
Posts: 291
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Re: abinit 7.2.1 with openmpi

Post by gmatteo » Sun May 26, 2013 2:18 pm

configure:17102: ./conftest
./conftest: error while loading shared libraries: libmpi_f90.so.0: cannot open shared object file: No such file or directory
configure:17102: $? = 127
configure: program exited with status 127

mpif90 cannot find the shared library libmpi_f90.so.0.

I guess the library is located somewhere in one of the directories in /home/soft/mpi/openmpi-142-intel/
Perhaps in /home/soft/mpi/openmpi-142-intel/lib/intel64/ (not sure, since I've never used intel MPI)

Before running configure, you have to modify the environment variable LD_LIBRARY_PATH
by adding all the directories that contain the libraries you need, e.g.

export LD_LIBRARY_PATH=/home/soft/mpi/openmpi-142-intel/add_the_path_to_the_directory_with_libmpi:$LD_LIBRARY_PATH
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abinitfonda
Posts: 3
Joined: Sun May 19, 2013 12:41 pm

Re: abinit 7.2.1 with openmpi

Post by abinitfonda » Mon May 27, 2013 7:50 am

gmatteo wrote:configure:17102: ./conftest
./conftest: error while loading shared libraries: libmpi_f90.so.0: cannot open shared object file: No such file or directory
configure:17102: $? = 127
configure: program exited with status 127

mpif90 cannot find the shared library libmpi_f90.so.0.

Before running configure, you have to modify the environment variable LD_LIBRARY_PATH
by adding all the directories that contain the libraries you need, e.g.

export LD_LIBRARY_PATH=/home/soft/mpi/openmpi-142-intel/add_the_path_to_the_directory_with_libmpi:$LD_LIBRARY_PATH


Thanks, gmatteo, it works!

Now I came across another problem with "clock-gettime", like

Code: Select all

/home/soft/abinit-7.2.1/builder/fallbacks/exports/lib/libdft_common.a(utils.o): In function `nanosec_':
/home/soft/abinit-7.2.1/builder/fallbacks/sources/bigdft-abi-1.0.4/src/utils.c:53: undefined reference to `clock_gettime'
make[3]: *** [abinit] Error 1
make[3]: Leaving directory `/home/soft/abinit-7.2.1/builder/src/98_main'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/soft/abinit-7.2.1/builder/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/soft/abinit-7.2.1/builder'
make: *** [all] Error 2


Do you have some idea? Or anybody else? Thanks in advance!

Ted
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