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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/psconda.sh
# If a different environment needs to be activated, it needs to be activated here
# before setup_testrel.
see New Style Test Releases
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 -py2
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/conda_activate ana-4.0.37-py3
git clone git@github.com:lcls-psana/Detector.git
scons
clean_lcls1_env # from ~/bin/clean_lcls1_env
External Packages
If working on external packages (for example, ndarray, psalg, pdsdata, python), you need to also to check out the corresponding proxy package. For example: ndarray_ext, Python, psalg_ext, pdsdata_ext, etc. The Python proxy package allows the python header files to be visible to C++ code.
Production
source /cds/sw/ds/ana/conda1/manage/bin/psconda.sh -py3py2
defaults to py2py3, optionally add a a "-py3" flag for py3py2" flag for py2
List release package tags
For example ana-4.0.45 tags can be seen in
/cds/sw/ds/ana/conda1/inst/envs/ana-4.0.45/data/anarelinfo/psana-conda-tags
Change test release
List available release by command
conde env list
Then set desired release ana-4.0.## with script/command conda_activate.
Sequence of commands mast be:
source /cds/sw/ds/ana/conda1/manage/bin/psconda.sh
source conda_activate ana-4.0.##
source /cds/sw/ds/ana/conda1/manage/bin/setup_testrel
LCLS2
Development
cd mytestrel
source /cds/sw/ds/ana/conda2/manage/bin/psconda.sh
...
./clean_lcls2.sh
./build_all.sh
Change test release
List available release by command
conde env list
Then set desired release ps-4.5.## with commands
conda deactivate
conda activate ps-4.5.##
Production
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
Build ami2
ssh -Y psbuild-rhel7
git clone https://github.com/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
clone https://github.com/slac-lcls/ami.git
cd lcls2
source setup_env.sh
./build_all.sh
cd ../ami
./build_all.sh
ami-local -b 1 -f interval=1 psana://exp=tmoc00118,run=222,dir=/cds/data/psdm/prj/public01/xtc
ami Simple Introductory Examples
S3DF
lcls1:
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:
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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
on psana: export SIT_DATA=/cds/group/psdm/data
export SIT_DATA=/sdf/group/lcls/ds/ana/data
Ex:
sdfdtn001% detnames /sdf/data/lcls/ds/xpp/xpptut15/xtc/e665-r0240-s02-c00.xtc
/sdf/group/lcls/ds/ana/
data, detector, sw
FFB
lclc2:
to access /cds/data/drpsrcf/tst/tstx00117/xtc
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
chrisgit clone git@github.com:lcls-psana/.git