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Ticketing system for developers/testers and power users of the Brain Simulation Platform of the Human Brain Project
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Installation of bluepyopt on Marconi Broadwell and Galileo #522

Closed pramodk closed 4 years ago

pramodk commented 4 years ago

Here is the email:

As Marconi KNL is down at the moment, would it be possible that you or your
collaborators install BluePyOpt on Marconi Broadwell and Galileo?

Please let me know if it is possible and how long the process would take.

Related task: #533

pramodk commented 4 years ago

Here is how modules can be used:

Galileo

export MODULEPATH=$MODULEPATH:/gpfs/work/HBP_CDP21_it_1/pkumbhar/HBP/galileo/install/latest
module purge
module load anaconda/2019.07 python/3.6.4 py-bluepyopt

$ nrnivmodl .

$ python3
Python 3.6.4 (default, Feb 14 2018, 14:45:07)
...
>>> from neuron import h
>>> import bluepyopt as bpop
>>> import bluepyopt.ephys as ephys
>>> import matplotlib
>>> import numpy
>>>

Marconi Broadwell

export MODULEPATH=$MODULEPATH:/marconi_work/HBP_CDP2_it/pkumbhar/HBP/marconi/install/latest
module purge
module load python/3.6.4 anaconda && module unload python/3.6.4
module load python/3.6.4 py-bluepyopt py-matplotlib/3.1.1

$ nrnivmodl .

$ python3
Python 3.6.4 (default, Feb 14 2018, 14:45:07)
...
>>> from neuron import h
>>> import bluepyopt as bpop
>>> import bluepyopt.ephys as ephys
>>> import matplotlib
>>> import numpy
>>>
clupascu commented 4 years ago

Thank you @pramodk. I will test both and let you know.

SteMasoli commented 4 years ago

Marconi A2 (KNL) was under decommission starting with the 15th of january.

mmigliore commented 4 years ago

Correct. This is why BluePyOpt is being deployed and tested on the broadwell partition of Marconi and on Galileo.

Il gio 6 feb 2020, 10:00 Stefano notifications@github.com ha scritto:

Marconi A2 (KNL) was decommission in date 15th of january.

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clupascu commented 4 years ago

@pramodk the modules that you shared work fine on Marconi Broadwelll and Galileo through ssh. I am still waiting for the installation of Unicore in order to test the modules on Unicore too. I will update the ticket when the Unicore installation will be complete.

clupascu commented 4 years ago

@pramodk can you please install also on jureca the bluepyopt python3 version? Thank you. Please keep also the already available python2 version on jureca if possible.

alex4200 commented 4 years ago

@clupascu Needs to test the new installation

clupascu commented 4 years ago

@pramodk any news on the installation of bluepyopt python3 on jureca?

pramodk commented 4 years ago

@pramodk any news on the installation of bluepyopt python3 on jureca?

this was bit mixed with neuron3 installation in #525. Sorry.

@jorblancoa is enabling python3 module for bluepyopt as well and should be available as documented here. we will update here once that is done.

jorblancoa commented 4 years ago

It should be already available. Module name: py-bluepyopt/1.6.56-gcc-serial-python3

clupascu commented 4 years ago

When I load the above module on jureca I get

jorblancoa commented 4 years ago

Sorry I forgot to mention that you need to load 26-02 modules: module use /p/project/cvsk25/software-deployment/HBP/jureca-booster/26-02-2020/modules/tcl/linux-centos7-haswell module load py-bluepyopt/1.6.56-gcc-serial-python3

clupascu commented 4 years ago

Now my job fails with some errors

PSI: handleAnswer: spawn to node 3631 failed: "testExecutable: stat(ipengine): No such file or directory" Could not spawn 'ipengine' process 143: No such file or directory spawnSingleExecutable: PSI_spawn() failed. Unable to start all processes. Aborting. srun: error: jrc5631: tasks 0-23: Exited with exit code 2

clupascu commented 4 years ago

@pramodk opened a ticket on Jureca requesting the installation of some packages. Ipyparallel is one of the packages needed that was creating the error from my previous comment (I think).

pramodk commented 4 years ago

@clupascu : we started looking into this last friday and saw that some of the packages are missing on JURECA booster which were previously available. So we are checking if those can be installed.

alex4200 commented 4 years ago

Hi, can you please tick the boxes in the top-most main comment to mark the cases that are done?

pramodk commented 4 years ago

See #533, bluepyopt is installed on both systems.

clupascu commented 4 years ago

I am closing this issue. We will continue commenting on #533.