The mpi4py was installed by me with "pip install mpi4py" If I uninstall it, then run "which mpi4py" or "pydoc mpi4py", nothing is found. I don't understand *"**Stampede for instance has mvapich2 available which has mpi4py". * What do you mean and how can I enable it ? On Thu, Feb 11, 2016 at 12:12 AM, Tao Wang <twang15@ncsu.edu> wrote:
Hi, Tuomas
It is Stampede.
(firedrake) c559-703.stampede(20)$ ldd /work/03915/taoncsu/firedrake.impi/firedrake/lib/python2.7/site-packages/mpi4py/MPI.so linux-vdso.so.1 => (0x00007fff6c47f000) libdl.so.2 => /lib64/libdl.so.2 (0x00002aaf89bd3000) libpython2.7.so.1.0 => /home1/03915/taoncsu/tools/python/lib/libpython2.7.so.1.0 (0x00002aaf89dd7000) *libmpi.so.12 => /opt/apps/intel15/mvapich2/2.1/lib/libmpi.so.12* (0x00002aaf8a1b9000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00002aaf8abe6000) libc.so.6 => /lib64/libc.so.6 (0x00002aaf8ae03000) /lib64/ld-linux-x86-64.so.2 (0x0000003267200000) libutil.so.1 => /lib64/libutil.so.1 (0x00002aaf8b197000) libm.so.6 => /lib64/libm.so.6 (0x00002aaf8b39b000) libnuma.so.1 => /usr/lib64/libnuma.so.1 (0x00002aaf8b61f000) libxml2.so.2 => /usr/lib64/libxml2.so.2 (0x00002aaf8b82b000) libibmad.so.5 => /opt/ofed/lib64/libibmad.so.5 (0x00002aaf8bb7e000) librdmacm.so.1 => /opt/ofed/lib64/librdmacm.so.1 (0x00002aaf8bd95000) libibumad.so.3 => /opt/ofed/lib64/libibumad.so.3 (0x00002aaf8bf9d000) libibverbs.so.1 => /opt/ofed/lib64/libibverbs.so.1 (0x00002aaf8c1a4000) librt.so.1 => /lib64/librt.so.1 (0x00002aaf8c3b2000) libifport.so.5 => /opt/apps/intel/15/composer_xe_2015.2.164/compiler/lib/intel64/libifport.so.5 (0x00002aaf8c5ba000) libifcore.so.5 => /opt/apps/intel/15/composer_xe_2015.2.164/compiler/lib/intel64/libifcore.so.5 (0x00002aaf8c7e8000) libimf.so => /opt/apps/intel/15/composer_xe_2015.2.164/compiler/lib/intel64/libimf.so (0x00002aaf8cb1a000) libsvml.so => /opt/apps/intel/15/composer_xe_2015.2.164/compiler/lib/intel64/libsvml.so (0x00002aaf8cfd5000) libintlc.so.5 => /opt/apps/intel/15/composer_xe_2015.2.164/compiler/lib/intel64/libintlc.so.5 (0x00002aaf8dea9000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00002aaf8e104000) libz.so.1 => /work/03915/taoncsu/linuxbrew/lib/libz.so.1 (0x00002aaf8e31b000)
Then, I run
nm /opt/apps/intel15/mvapich2/2.1/lib/libmpi.so.12 | grep ompi_mpi_char
Nothing found. Thus, I supposed ompi_mpi_char is not in /opt/apps/intel15/mvapich2/2.1/lib/libmpi.so.12
Any ideas ?
On Wed, Feb 10, 2016 at 10:48 PM, Tuomas Karna <tuomas.karna@gmail.com> wrote:
Hi Tao,
May I ask which machine you are using?
Stampede for instance has mvapich2 available which has mpi4py, and works with PETSc/firedrake.
- Tuomas
On 02/10/2016 06:26 PM, Tao Wang wrote:
Since firedrake depends on mpi4py, which depends on open-mpi or mpich. But the server I used does not have them, only having intel mpi. The following is a test.
python -c "from mpi4py import MPI"
====*Error msg *==== Traceback (most recent call last): File "<string>", line 1, in <module> ImportError: /work/03915/taoncsu/firedrake.impi/firedrake/lib/python2.7/site-packages/mpi4py/MPI.so: undefined symbol: ompi_mpi_char
Then, I run nm /opt/apps/intel15/impi/5.0.2.044/intel64/lib/libmpi.so.12 <http://5.0.2.36/intel64/lib/libmpi.so.12> | grep ompi_mpi_char
Nothing is returned, it seems there is no such symbol in Intel MPI implementation.
Does this suggest that firedrake cannot work with intel mpi implementation ?
On Wed, Feb 10, 2016 at 8:43 PM, Tao Wang <twang15@ncsu.edu> wrote:
I failed to install it on CentOS with --no-package-manager option
Please see this issue <https://github.com/firedrakeproject/firedrake/issues/680#issuecomment-175511215> for more details. Could you answer my questions one by one ?
Thanks a lot for your help.
On Wed, Feb 10, 2016 at 5:50 PM, Miklós Homolya < <m.homolya14@imperial.ac.uk>m.homolya14@imperial.ac.uk> wrote:
Make sure you have all the other dependencies installed and then use the install script with the —no-package-manager option.
On 10 Feb 2016, at 22:28, Tao Wang < <twang15@ncsu.edu> twang15@ncsu.edu> wrote:
Hi, all
I notice firedrake has dependency on open-mpi. But, I want to use other mpi implementation. I already have impi installed on my machine.
What should I do to make this change happen ?
Thanks, Tao _______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
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