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Content
Table of Contents |
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Cloning packages from git
git clone git@github.com:slac-lcls/lcls2.git
git clone git@github.com:lcls-psana/Detector.git
git clone git@github.com:lcls-psana/PSCalib.git
git clone git@github.com:lcls-psana/CalibManager.git
git clone git@github.com:lcls-psana/pyimgalgos.git
git clone git@github.com:lcls-psana/.git
git clonegit@github.com:lcls-psana/SConsTools.git
git clone git@github.com:lcls-psana/pdsdata.git
git clone git@github.com:lcls-psana/psalg.git
git clone git@github.com:lcls-psana/data_test.git /tmp/data_test
git clone git@github.com:slaclab/anarel-manage.git manage
git clone git@github.com:slac-lcls/psana1-feedstock.git
git clone https://github.com/slac-lcls/psana1-feedstock
PCDS
LCLS1
Development
cd mytestrel
rm .sit_conda_env
...
source /cds/sw/ds/ana/conda1/manage/bin/setup_testrel
### defaults to py2py3, optionally add a a "-py3py2" flag for py3flag for py2
source /cds/sw/ds/ana/conda1/manage/bin/psconda.sh -py3py2
Note |
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Since 2022-09-15 ana-5.0.45 Python 3 is now the default |
Note |
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Since ana-4.0.48-py3 for python 3.9 git clone git@github.com:lcls-psana/boost git clone git@github.com:lcls-psana/python |
source /cds/sw/ds/ana/conda1/manage/bin/setup_testrel
...
source /cds/sw/ds/ana/conda1/manage/bin/psconda.sh -py3py2
defaults to py2py3, optionally add a a "-py3py2" flag for py3flag for py2
List release package tags
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Sequence of commands mast be:
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:
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git clone git@github.com:lcls-psana/python
source /cds/sw/ds/ana/conda1/manage/bin/psconda.sh
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source /cds/sw/ds/ana/conda1/manage/bin/setup_testrel
LCLS2
Development
cd mytestrel
source /cds/sw/ds/ana/conda2/manage/bin/psconda.sh
...
source /reg/g/pcds/dist/pds/ued/scripts/setup_env.sh
Clone packages from git
git clone git@github.com:slac-lcls/lcls2.git
git clone git@github.com:lcls-psana/Detector.git
git clone git@github.com:lcls-psana/PSCalib.git
git clone git@github.com:lcls-psana/CalibManager.git
git clone git@github.com:lcls-psana/pyimgalgos.git
git clone git@github.com:lcls-psana/.git
Build ami2
ssh -Y psbuild-rhel7
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source /sdf/group/lcls/ds/ana/sw/conda1/manage/bin/psconda.sh [ -py2]
source /sdf/group/lcls/ds/ana/sw/conda1/manage/bin/psconda.sh
source /sdf/group/lcls/ds/ana/sw/conda1/manage/bin/setup_testrel
lclc2:
Code Block | ||||
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unset LD_LIBRARY_PATH unset PYTHONPATH # for psana #source /cds/sw/ds/ana/conda2-v2/inst/etc/profile.d/conda.sh #export CONDA_ENVS_DIRS=/cds/sw/ds/ana/conda2/inst/envs/ # for s3df source /sdf/group/lcls/ds/ana/sw/conda2/inst/etc/profile.d/conda.sh export CONDA_ENVS_DIRS=/sdf/group/lcls/ds/ana/sw/conda2/inst/envs # Mikhail: root of psdm directories export DIR_PSDM=/sdf/group/lcls/ds/ana/ export SIT_PSDM_DATA=/sdf/data/lcls/ds/ conda activate ps-4.5.26 RELDIR="$( cd "$( dirname $(readlink -f "${BASH_SOURCE[0]}") )" && pwd )" export PATH=$RELDIR/install/bin:${PATH} pyver=$(python -c "import sys; print(str(sys.version_info.major)+'.'+str(sys.version_info.minor))") export PYTHONPATH=$RELDIR/install/lib/python$pyver/site-packages # for procmgr export TESTRELDIR=$RELDIR/install export PROCMGR_EXPORT=RDMAV_FORK_SAFE=1,RDMAV_HUGEPAGES_SAFE=1 # See fi_verbs man page regarding fork() # cpo: seems that in more recent versions blas is creating many threads export OPENBLAS_NUM_THREADS=1 # cpo: getting intermittent file-locking issue on ffb, so try this export HDF5_USE_FILE_LOCKING=FALSE # for libfabric. decreases performance a little, but allows forking export RDMAV_FORK_SAFE=1 export RDMAV_HUGEPAGES_SAFE=1 # Mikhail: root of psdm directories #export DIR_PSDM=/cds/group/psdm # cpo: workaround a qt bug which may no longer be there (dec 5, 2022) if [ ! -d /usr/share/X11/xkb ]; then export QT_XKB_CONFIG_ROOT=${CONDA_PREFIX}/lib fi # needed by Ric to get correct libfabric man pages export MANPATH=$CONDA_PREFIX/share/man${MANPATH:+:${MANPATH}} |
for developers: source lcls2/setup_env.sh
for users: source /sdf/group/lcls/ds/ana/sw/conda2/manage/bin/psconda.sh
...
It’s “ssh psffb”. add the “dir=“ option to DataSource, or “export SIT_PSDM_DATA=/cds/data/drpsrcf”
SLURM commands
sinfo -N -r -l
squeue -u $USER | grep 197 | awk '{print $1}' | xargs -n 1 scancel
squeue -u <username>
scancel <job_id>
scontrol show partition <partition>
scontrol show node <hostname>
scontrol show job <job_id>
scontrol hold <job_list>
scontrol release <job_list>
scontrol show hostnames
sinfo --states=idle
Reservation of batch host for individual work
srun --partition milano --nodelist=sdfmilan112 --account lcls:prjdat21 -n 1 --time=02:00:00 --exclusive --pty /bin/bash
srun --partition milano --account lcls:prjdat21 -n 1 --time=02:00:00 --exclusive --pty /bin/bash
srun --partition milano --reservation=lcls:scaling --account lcls:prjdat21 -n 1 --time=02:00:00 --exclusive --pty /bin/bash
Patching release
on pcds
> s3dflogin
> pslogin
ssh psbuild-rhel7-01 -l psreldev
source /cds/sw/ds/ana/conda1/manage/bin/psconda.sh
on s3df
>s3dflogin
ssh psana -l psreldev
source /sdf/group/lcls/ds/ana/sw/conda1/manage/bin/psconda.sh
Patching
conda deactivate
conda env list
conda activate ana-4.0.51-py3
2023-09-15 O'Grady, Paul Christopher <cpo@slac.stanford.edu> To: Dubrovin, Mikhail
For the log the patch commands are below:
(ana-4.0.51-py3) pwd
/sdf/group/lcls/ds/ana/sw/conda1/inst/envs/ana-4.0.51-py3/lib/python3.9/site-packages/Detector
(ana-4.0.51-py3) cp ~cpo/git/Detector/src/AreaDetector.py AreaDetector.py
(ana-4.0.51-py3) cd ../PSCalib/
(ana-4.0.51-py3) cp ~cpo/git/PSCalib/src/GlobalUtils.py GlobalUtils.py
chris