Hi All, I've just updated the common install of yt on Kraken to 2.1, and added an install of the unstable branch. Both are full copies of yt that is kept on lustre in a non-volatile place. This means that it is accessible from both the login nodes and the compute nodes, but unlike most files on Lustre, will not be deleted automatically. If you wish to use yt 2.1, which will only see changes for bug fixes, please set your environment using these settings: YT_DEST => /lustre/scratch/proj/yt_common/2.1 PATH => /lustre/scratch/proj/yt_common/2.1/bin/ PYTHONPATH => /lustre/scratch/proj/yt_common/2.1/lib/python2.7/site-packages/ LD_LIBRARY_PATH => /lustre/scratch/proj/yt_common/2.1/lib/ If you wish to use the unstable branch, which I'll update on Kraken when I remember to do it (or you can bug me if I haven't): YT_DEST => /lustre/scratch/proj/yt_common/unstable PATH => /lustre/scratch/proj/yt_common/unstable/bin/ PYTHONPATH => /lustre/scratch/proj/yt_common/unstable/lib/python2.7/site-packages/ LD_LIBRARY_PATH => /lustre/scratch/proj/yt_common/unstable/lib/ The older versions of yt at /lustre/scratch/proj/yt_common/2.0 and /lustre/scratch/proj/yt_common/trunk will be deleted within a week or so. -- Stephen Skory s@skory.us http://stephenskory.com/ 510.621.3687 (google voice)
I guess this would be a sort of followup to Stephen's email of running YT on Kraken, here's what I figured out combined with what I got from the system admin: Installing mpi4py can be a little more troublesome because there's no mpicc wrapper, you'll have to edit the mpi.cfg file and put in: mpicc = gcc -lmpi mpicxx = g++ -lmpi++ -lmpi then do: python setup.py build --mpi=<your mpi section name in mpi.cfg> python setup.py install (following http://mpi4py.scipy.org/docs/usrman/install.html) next you'll have to set these environment variables, I have it in a .bashrc and source it every time I log into Nautilus. module swap mpt mpt/2.03 export MPI_SHARED_NEIGHBORHOOD=HOST Last but not least, the system admin told me SGI identified a bug so that mpi at least under python works for only up to 8 processors. I've tried 16 and failed, tried 8 and ran, so I believe their story. so under an interactive queue, you'll want to do something like: mpiexec -np 8 python script.py --parallel to run YT in parallel Hope this helps From G.S.
Hi All,
I've just updated the common install of yt on Kraken to 2.1, and added an install of the unstable branch. Both are full copies of yt that is kept on lustre in a non-volatile place. This means that it is accessible from both the login nodes and the compute nodes, but unlike most files on Lustre, will not be deleted automatically.
If you wish to use yt 2.1, which will only see changes for bug fixes, please set your environment using these settings:
YT_DEST => /lustre/scratch/proj/yt_common/2.1 PATH => /lustre/scratch/proj/yt_common/2.1/bin/ PYTHONPATH => /lustre/scratch/proj/yt_common/2.1/lib/python2.7/site-packages/ LD_LIBRARY_PATH => /lustre/scratch/proj/yt_common/2.1/lib/
If you wish to use the unstable branch, which I'll update on Kraken when I remember to do it (or you can bug me if I haven't):
YT_DEST => /lustre/scratch/proj/yt_common/unstable PATH => /lustre/scratch/proj/yt_common/unstable/bin/ PYTHONPATH => /lustre/scratch/proj/yt_common/unstable/lib/python2.7/site-packages/ LD_LIBRARY_PATH => /lustre/scratch/proj/yt_common/unstable/lib/
The older versions of yt at /lustre/scratch/proj/yt_common/2.0 and /lustre/scratch/proj/yt_common/trunk will be deleted within a week or so.
-- Stephen Skory s@skory.us http://stephenskory.com/ 510.621.3687 (google voice) _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
I guess this would be a sort of followup to Stephen's email of running YT on Kraken, here's what I figured out combined with what I got from the system admin: Installing mpi4py can be a little more troublesome because there's no mpicc wrapper, you'll have to edit the mpi.cfg file and put in: mpicc = gcc -lmpi mpicxx = g++ -lmpi++ -lmpi then do: python setup.py build --mpi=<your mpi section name in mpi.cfg> python setup.py install (following http://mpi4py.scipy.org/docs/usrman/install.html) next you'll have to set these environment variables, I have it in a .bashrc and source it every time I log into Nautilus. module swap mpt mpt/2.03 export MPI_SHARED_NEIGHBORHOOD=HOST Last but not least, the system admin told me SGI identified a bug so that mpi at least under python works for only up to 8 processors. I've tried 16 and failed, tried 8 and ran, so I believe their story. so under an interactive queue, you'll want to do something like: mpiexec -np 8 python script.py --parallel to run YT in parallel Hope this helps From G.S.
Hi All,
I've just updated the common install of yt on Kraken to 2.1, and added an install of the unstable branch. Both are full copies of yt that is kept on lustre in a non-volatile place. This means that it is accessible from both the login nodes and the compute nodes, but unlike most files on Lustre, will not be deleted automatically.
If you wish to use yt 2.1, which will only see changes for bug fixes, please set your environment using these settings:
YT_DEST => /lustre/scratch/proj/yt_common/2.1 PATH => /lustre/scratch/proj/yt_common/2.1/bin/ PYTHONPATH => /lustre/scratch/proj/yt_common/2.1/lib/python2.7/site-packages/ LD_LIBRARY_PATH => /lustre/scratch/proj/yt_common/2.1/lib/
If you wish to use the unstable branch, which I'll update on Kraken when I remember to do it (or you can bug me if I haven't):
YT_DEST => /lustre/scratch/proj/yt_common/unstable PATH => /lustre/scratch/proj/yt_common/unstable/bin/ PYTHONPATH => /lustre/scratch/proj/yt_common/unstable/lib/python2.7/site-packages/ LD_LIBRARY_PATH => /lustre/scratch/proj/yt_common/unstable/lib/
The older versions of yt at /lustre/scratch/proj/yt_common/2.0 and /lustre/scratch/proj/yt_common/trunk will be deleted within a week or so.
-- Stephen Skory s@skory.us http://stephenskory.com/ 510.621.3687 (google voice) _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
I believe YT is installed on nautilus globally. If you want to use YT on Nautilus you can get your environment set up by executing "module load yt" from the command line. mpi4py and all that should already be there. Dave Semeraro ----- Original Message -----
I guess this would be a sort of followup to Stephen's email of running YT on Kraken, here's what I figured out combined with what I got from the system admin:
Installing mpi4py can be a little more troublesome because there's no mpicc wrapper, you'll have to edit the mpi.cfg file and put in:
mpicc = gcc -lmpi mpicxx = g++ -lmpi++ -lmpi
then do: python setup.py build --mpi=<your mpi section name in mpi.cfg> python setup.py install
(following http://mpi4py.scipy.org/docs/usrman/install.html)
next you'll have to set these environment variables, I have it in a .bashrc and source it every time I log into Nautilus.
module swap mpt mpt/2.03 export MPI_SHARED_NEIGHBORHOOD=HOST
Last but not least, the system admin told me SGI identified a bug so that mpi at least under python works for only up to 8 processors. I've tried 16 and failed, tried 8 and ran, so I believe their story.
so under an interactive queue, you'll want to do something like: mpiexec -np 8 python script.py --parallel to run YT in parallel
Hope this helps
From G.S.
Hi All,
I've just updated the common install of yt on Kraken to 2.1, and added an install of the unstable branch. Both are full copies of yt that is kept on lustre in a non-volatile place. This means that it is accessible from both the login nodes and the compute nodes, but unlike most files on Lustre, will not be deleted automatically.
If you wish to use yt 2.1, which will only see changes for bug fixes, please set your environment using these settings:
YT_DEST => /lustre/scratch/proj/yt_common/2.1 PATH => /lustre/scratch/proj/yt_common/2.1/bin/ PYTHONPATH => /lustre/scratch/proj/yt_common/2.1/lib/python2.7/site-packages/ LD_LIBRARY_PATH => /lustre/scratch/proj/yt_common/2.1/lib/
If you wish to use the unstable branch, which I'll update on Kraken when I remember to do it (or you can bug me if I haven't):
YT_DEST => /lustre/scratch/proj/yt_common/unstable PATH => /lustre/scratch/proj/yt_common/unstable/bin/ PYTHONPATH => /lustre/scratch/proj/yt_common/unstable/lib/python2.7/site-packages/ LD_LIBRARY_PATH => /lustre/scratch/proj/yt_common/unstable/lib/
The older versions of yt at /lustre/scratch/proj/yt_common/2.0 and /lustre/scratch/proj/yt_common/trunk will be deleted within a week or so.
-- Stephen Skory s@skory.us http://stephenskory.com/ 510.621.3687 (google voice) _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Sorry I should have made it more clear, the install script I was referring to is the YT 2.1 dev version, the one already installed on Nautilus is 1.7. From G.S.
I believe YT is installed on nautilus globally. If you want to use YT on Nautilus you can get your environment set up by executing "module load yt" from the command line. mpi4py and all that should already be there.
Dave Semeraro
----- Original Message -----
I guess this would be a sort of followup to Stephen's email of running YT on Kraken, here's what I figured out combined with what I got from the system admin:
Installing mpi4py can be a little more troublesome because there's no mpicc wrapper, you'll have to edit the mpi.cfg file and put in:
mpicc = gcc -lmpi mpicxx = g++ -lmpi++ -lmpi
then do: python setup.py build --mpi=<your mpi section name in mpi.cfg> python setup.py install
(following http://mpi4py.scipy.org/docs/usrman/install.html)
next you'll have to set these environment variables, I have it in a .bashrc and source it every time I log into Nautilus.
module swap mpt mpt/2.03 export MPI_SHARED_NEIGHBORHOOD=HOST
Last but not least, the system admin told me SGI identified a bug so that mpi at least under python works for only up to 8 processors. I've tried 16 and failed, tried 8 and ran, so I believe their story.
so under an interactive queue, you'll want to do something like: mpiexec -np 8 python script.py --parallel to run YT in parallel
Hope this helps
From G.S.
Hi All,
I've just updated the common install of yt on Kraken to 2.1, and added an install of the unstable branch. Both are full copies of yt that is kept on lustre in a non-volatile place. This means that it is accessible from both the login nodes and the compute nodes, but unlike most files on Lustre, will not be deleted automatically.
If you wish to use yt 2.1, which will only see changes for bug fixes, please set your environment using these settings:
YT_DEST => /lustre/scratch/proj/yt_common/2.1 PATH => /lustre/scratch/proj/yt_common/2.1/bin/ PYTHONPATH => /lustre/scratch/proj/yt_common/2.1/lib/python2.7/site-packages/ LD_LIBRARY_PATH => /lustre/scratch/proj/yt_common/2.1/lib/
If you wish to use the unstable branch, which I'll update on Kraken when I remember to do it (or you can bug me if I haven't):
YT_DEST => /lustre/scratch/proj/yt_common/unstable PATH => /lustre/scratch/proj/yt_common/unstable/bin/ PYTHONPATH => /lustre/scratch/proj/yt_common/unstable/lib/python2.7/site-packages/ LD_LIBRARY_PATH => /lustre/scratch/proj/yt_common/unstable/lib/
The older versions of yt at /lustre/scratch/proj/yt_common/2.0 and /lustre/scratch/proj/yt_common/trunk will be deleted within a week or so.
-- Stephen Skory s@skory.us http://stephenskory.com/ 510.621.3687 (google voice) _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
no problem. I requested NICS update their 1.7 to the latest stable version. ----- Original Message -----
Sorry I should have made it more clear, the install script I was referring to is the YT 2.1 dev version, the one already installed on Nautilus is 1.7.
From G.S.
I believe YT is installed on nautilus globally. If you want to use YT on Nautilus you can get your environment set up by executing "module load yt" from the command line. mpi4py and all that should already be there.
Dave Semeraro
----- Original Message -----
I guess this would be a sort of followup to Stephen's email of running YT on Kraken, here's what I figured out combined with what I got from the system admin:
Installing mpi4py can be a little more troublesome because there's no mpicc wrapper, you'll have to edit the mpi.cfg file and put in:
mpicc = gcc -lmpi mpicxx = g++ -lmpi++ -lmpi
then do: python setup.py build --mpi=<your mpi section name in mpi.cfg> python setup.py install
(following http://mpi4py.scipy.org/docs/usrman/install.html)
next you'll have to set these environment variables, I have it in a .bashrc and source it every time I log into Nautilus.
module swap mpt mpt/2.03 export MPI_SHARED_NEIGHBORHOOD=HOST
Last but not least, the system admin told me SGI identified a bug so that mpi at least under python works for only up to 8 processors. I've tried 16 and failed, tried 8 and ran, so I believe their story.
so under an interactive queue, you'll want to do something like: mpiexec -np 8 python script.py --parallel to run YT in parallel
Hope this helps
From G.S.
Hi All,
I've just updated the common install of yt on Kraken to 2.1, and added an install of the unstable branch. Both are full copies of yt that is kept on lustre in a non-volatile place. This means that it is accessible from both the login nodes and the compute nodes, but unlike most files on Lustre, will not be deleted automatically.
If you wish to use yt 2.1, which will only see changes for bug fixes, please set your environment using these settings:
YT_DEST => /lustre/scratch/proj/yt_common/2.1 PATH => /lustre/scratch/proj/yt_common/2.1/bin/ PYTHONPATH => /lustre/scratch/proj/yt_common/2.1/lib/python2.7/site-packages/ LD_LIBRARY_PATH => /lustre/scratch/proj/yt_common/2.1/lib/
If you wish to use the unstable branch, which I'll update on Kraken when I remember to do it (or you can bug me if I haven't):
YT_DEST => /lustre/scratch/proj/yt_common/unstable PATH => /lustre/scratch/proj/yt_common/unstable/bin/ PYTHONPATH => /lustre/scratch/proj/yt_common/unstable/lib/python2.7/site-packages/ LD_LIBRARY_PATH => /lustre/scratch/proj/yt_common/unstable/lib/
The older versions of yt at /lustre/scratch/proj/yt_common/2.0 and /lustre/scratch/proj/yt_common/trunk will be deleted within a week or so.
-- Stephen Skory s@skory.us http://stephenskory.com/ 510.621.3687 (google voice) _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
participants (3)
-
Dave Semeraro -
gso＠physics.ucsd.edu -
Stephen Skory