Hi Tao,
On 02/10/2016 10:59 PM, Tao Wang wrote:
OK, great! We've made some progress. Yes you'll need to rebuild firedrake.Hi, Tuomas,
I remember this python(~/tools/python/bin/python) was installed by me.
Because, the first I login to Stampede, I found `which python` gave me "/usr/bin/python", Python 2.6.6. It is too old for me to install firedrake. So I build one and install it under my home. I was not aware there is a python (/opt/apps/intel15/python/2.7.9/bin/python) new enough for firedrake until you showed me.
It is easy to set python to /opt/apps/intel15/python/2.7.9/bin/python.But, I failed to make "pip list" to find mpi4py after just set the $PATH=/opt/apps/intel15/python/2.7.9/bin:$PATH
I tried another way
module load python/2.7.9The both python and mpi4py shows as yours.
But, the "make test" under firedrake directory fails. I guess firedrake has to be rebuilt from scratch.I will update
I think this worked for me earlier:
export PETSC_CONFIGURE_OPTIONS="--with-blas-lapack-dir=$MKLROOT"
python firedrake-install --developer --no-package-manager --log
The first line tells petsc to use intel mkl blas and lapack, $MKLROOT should point to the right dir.
On Thu, Feb 11, 2016 at 1:25 AM, Tao Wang <twang15@ncsu.edu> wrote:
Hi, TuomasThe following is the output:
c559-703.stampede(33)$ module list
Currently Loaded Modules:1) intel/15.0.2 2) mvapich2/2.1 3) xalt/0.6 4) TACC
c559-703.stampede(34)$ pip listapipkg (1.4)Cython (0.23.4)decorator (4.0.6)execnet (1.4.1)flake8 (2.5.1)mccabe (0.3.1)mpi4py (2.0.0)networkx (1.10)numpy (1.10.4)pep8 (1.7.0)petsc4py (3.6.0)pip (8.0.2)pudb (2015.4.1)py (1.4.31)pyflakes (1.0.0)Pygments (2.1)pytest (2.8.5)pytest-xdist (1.13.1)setuptools (19.4)triangle (2015.12.14)urwid (1.3.1)virtualenv (14.0.1)wheel (0.26.0)c559-703.stampede(35)$ pip show mpi4py---Metadata-Version: 2.0Name: mpi4pyVersion: 2.0.0Summary: Python bindings for MPIHome-page: https://bitbucket.org/mpi4py/mpi4py/Author: Lisandro DalcinAuthor-email: dalcinl@gmail.comLicense: BSDLocation: /home1/03915/taoncsu/tools/python/lib/python2.7/site-packagesRequires:c559-703.stampede(36)$ $python -c "import mpi4py; print mpi4py.__path__"-bash: -c: command not foundc559-703.stampede(37)$ python -c "import mpi4py; print mpi4py.__path__"['/home1/03915/taoncsu/tools/python/lib/python2.7/site-packages/mpi4py']c559-703.stampede(38)$ which python~/tools/python/bin/python
Apparently, the mpy4py and python are not the same to yours.I am curious about what makes these differences. It seems something is wrong with my .bashrc
On Thu, Feb 11, 2016 at 12:36 AM, Tuomas Karna <tuomas.karna@gmail.com> wrote:
Hi Tao,
Also on Stampede, I have loaded the following modules:
$module list
Currently Loaded Modules:
1) xalt/0.6 3) intel/15.0.2 5) phdf5/1.8.16 7) netcdf/4.3.3.1 (m)
2) TACC 4) mvapich2/2.1 6) python/2.7.9 8) pmetis/4.0.2
Python picks up the right mpi4py (virtualenv is not active):
$pip list
...
mpi4py (1.3.1)
...
$pip show mpi4py
---
Metadata-Version: 1.1
Name: mpi4py
Version: 1.3.1
Summary: MPI for Python
Home-page: http://mpi4py.googlecode.com/
Author: Lisandro Dalcin
Author-email: dalcinl@gmail.com
License: BSD
Location: /opt/apps/intel15/mvapich2_2_1/python/2.7.9/lib/python2.7/site-packages
Requires:
$python -c "import mpi4py; print mpi4py.__path__"
['/opt/apps/intel15/mvapich2_2_1/python/2.7.9/lib/python2.7/site-packages/mpi4py']
$which python
/opt/apps/intel15/python/2.7.9/bin/python
Could you try if you can reproduce these? You might be using wrong python for instance.
Cheers,
Tuomas
On 02/10/2016 09:21 PM, Tao Wang wrote:
The mpi4py was installed by me with "pip install mpi4py"
If I uninstall it, then run "which mpi4py" or "pydoc mpi4py", nothing is found.I don't understand "Stampede for instance has mvapich2 available which has mpi4py".
What do you mean and how can I enable it ?
On Thu, Feb 11, 2016 at 12:12 AM, Tao Wang <twang15@ncsu.edu> wrote:
Hi, Tuomas
It is Stampede.
(firedrake) c559-703.stampede(20)$ ldd /work/03915/taoncsu/firedrake.impi/firedrake/lib/python2.7/site-packages/mpi4py/MPI.solinux-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 runnm /opt/apps/intel15/impi/5.0.2.044/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 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> 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> 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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