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Improve how the environment is sourced from modules.sh

Benedikt Steinbusch requested to merge bs-env-filter into master

The first commit removes the filter that would only import certain variables defined by modules.sh (and also improves the way the env output is consumed so multi-line values are handled correctly). This is a diff between srun -pdevelbooster xenv | sort before and after the first commit.

--- xenv/old_env	2022-03-17 16:52:54.196855663 +0100
+++ xenv/new_env	2022-03-17 17:05:54.424112380 +0100
@@ -8,15 +8,15 @@
 ARCHIVE_jsc=/p/arch/zam
 ARCHIVE_jzam04=/p/arch/jzam04
 ARCHIVE_swmanage=/p/arch/swmanage
-BASH_ENV=/p/software/jurecadc/lmod/lmod/init/bash
+BASH_ENV=/p/software/jurecabooster/lmod/lmod/init/bash
 BASH_FUNC_jutil%%=() {  if [ $# -ge 1 ] && [ "$1" = "env" ]; then
 BASH_FUNC_ml%%=() {  eval $($LMOD_DIR/ml_cmd "$@")
 BASH_FUNC_module%%=() {  eval $($LMOD_CMD bash "$@") && eval $(${LMOD_SETTARG_CMD:-:} -s sh)
 BASH_FUNC_which%%=() {  ( alias;
-_=/bin/srun
-CMAKE_LIBRARY_PATH=/p/software/jurecadc/stages/2022/software/GCCcore/11.2.0/lib64
-CMAKE_PREFIX_PATH=/p/software/jurecadc/stages/2022/software/binutils/2.37-GCCcore-11.2.0:/p/software/jurecadc/stages/2022/software/zlib/1.2.11-GCCcore-11.2.0:/p/software/jurecadc/stages/2022/software/GCCcore/11.2.0
-CPATH=/p/software/jurecadc/stages/2022/software/binutils/2.37-GCCcore-11.2.0/include:/p/software/jurecadc/stages/2022/software/zlib/1.2.11-GCCcore-11.2.0/include
+_=/bin/env
+CMAKE_LIBRARY_PATH=/p/software/jurecabooster/stages/2022/software/GCCcore/11.2.0/lib64:/p/software/jurecadc/stages/2022/software/GCCcore/11.2.0/lib64
+CMAKE_PREFIX_PATH=/p/software/jurecabooster/stages/2022/software/zlib/1.2.11-GCCcore-11.2.0:/p/software/jurecabooster/stages/2022/software/binutils/2.37-GCCcore-11.2.0:/p/software/jurecabooster/stages/2022/software/GCCcore/11.2.0:/p/software/jurecadc/stages/2022/software/binutils/2.37-GCCcore-11.2.0:/p/software/jurecadc/stages/2022/software/zlib/1.2.11-GCCcore-11.2.0:/p/software/jurecadc/stages/2022/software/GCCcore/11.2.0
+CPATH=/p/software/jurecabooster/stages/2022/software/zlib/1.2.11-GCCcore-11.2.0/include:/p/software/jurecabooster/stages/2022/software/binutils/2.37-GCCcore-11.2.0/include:/p/software/jurecadc/stages/2022/software/binutils/2.37-GCCcore-11.2.0/include:/p/software/jurecadc/stages/2022/software/zlib/1.2.11-GCCcore-11.2.0/include
 CSCRATCH_ccstao=/p/cscratch/fs/ccstao
 CSCRATCH_chpsadm=/p/cscratch/fs/chpsadm
 DATA_hpsadm=/p/largedata/hpsadm
@@ -49,10 +49,10 @@
 JUTIL_ENV_VARS=ARCHIVE_jsc,ARCHIVE_jzam04,ARCHIVE_swmanage,HOME,ARCHIVE_cstao,ARCHIVE_hpsadm,PROJECT_cjsc,PROJECT_cdeep,PROJECT_ccstao,PROJECT_chpsadm,PROJECT_cjzam04,PROJECT_cparateam,PROJECT_JSCbenchmark,SCRATCH_cjsc,SCRATCH_cdeep,SCRATCH_ccstao,SCRATCH_chpsadm,SCRATCH_cjzam04,SCRATCH_cparateam,SCRATCH_JSCbenchmark,FASTDATA_jsc,FASTDATA_hpsadm,DATA_jsc,DATA_hpsadm,DATA_jzam04,CSCRATCH_ccstao,FASTDATA_swmanage,USERSOFTWARE_swmanage,CSCRATCH_chpsadm,SCRATCH_training2126,PROJECT_training2126
 LANG=en_US.UTF-8
 LC_CTYPE=en_US.UTF-8
-LD_LIBRARY_PATH=/p/software/jurecadc/stages/2022/software/binutils/2.37-GCCcore-11.2.0/lib:/p/software/jurecadc/stages/2022/software/zlib/1.2.11-GCCcore-11.2.0/lib:/p/software/jurecadc/stages/2022/software/GCCcore/11.2.0/lib64
+LD_LIBRARY_PATH=/p/software/jurecabooster/stages/2022/software/zlib/1.2.11-GCCcore-11.2.0/lib:/p/software/jurecabooster/stages/2022/software/binutils/2.37-GCCcore-11.2.0/lib:/p/software/jurecabooster/stages/2022/software/GCCcore/11.2.0/lib64:/p/software/jurecadc/stages/2022/software/binutils/2.37-GCCcore-11.2.0/lib:/p/software/jurecadc/stages/2022/software/zlib/1.2.11-GCCcore-11.2.0/lib:/p/software/jurecadc/stages/2022/software/GCCcore/11.2.0/lib64
 LESSOPEN=||/usr/bin/lesspipe.sh %s
-LIBRARY_PATH=/p/software/jurecadc/stages/2022/software/binutils/2.37-GCCcore-11.2.0/lib:/p/software/jurecadc/stages/2022/software/zlib/1.2.11-GCCcore-11.2.0/lib
-_LMFILES_=/p/software/jurecadc/productionstages/Stages/2022.lua:/p/software/jurecadc/stages/2022/UI/Compilers/GCCcore/.11.2.0.lua:/p/software/jurecadc/stages/2022/modules/all/Compiler/GCCcore/11.2.0/zlib/.1.2.11.lua:/p/software/jurecadc/stages/2022/modules/all/Compiler/GCCcore/11.2.0/binutils/.2.37.lua:/p/software/jurecadc/stages/2022/UI/Tools/StdEnv/2022.lua
+LIBRARY_PATH=/p/software/jurecabooster/stages/2022/software/zlib/1.2.11-GCCcore-11.2.0/lib:/p/software/jurecabooster/stages/2022/software/binutils/2.37-GCCcore-11.2.0/lib:/p/software/jurecadc/stages/2022/software/binutils/2.37-GCCcore-11.2.0/lib:/p/software/jurecadc/stages/2022/software/zlib/1.2.11-GCCcore-11.2.0/lib
+_LMFILES_=/p/software/jurecabooster/productionstages/Stages/2022.lua:/p/software/jurecabooster/stages/2022/UI/Compilers/GCCcore/.11.2.0.lua:/p/software/jurecabooster/stages/2022/modules/all/Compiler/GCCcore/11.2.0/binutils/.2.37.lua:/p/software/jurecabooster/stages/2022/UI/Tools/StdEnv/2022.lua:/p/software/jurecabooster/stages/2022/modules/all/Compiler/GCCcore/11.2.0/zlib/.1.2.11.lua
 LMOD_arch=x86_64
 LMOD_AVAIL_STYLE=labels
 LMOD_CMD=/p/software/jurecabooster/lmod/8.4.1/libexec/lmod
@@ -77,29 +77,29 @@
 LOGNAME=steinbusch1
 LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=01;05;37;41:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.zst=01;31:*.tzst=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.wim=01;31:*.swm=01;31:*.dwm=01;31:*.esd=01;31:*.jpg=01;35:*.jpeg=01;35:*.mjpg=01;35:*.mjpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=01;36:*.au=01;36:*.flac=01;36:*.m4a=01;36:*.mid=01;36:*.midi=01;36:*.mka=01;36:*.mp3=01;36:*.mpc=01;36:*.ogg=01;36:*.ra=01;36:*.wav=01;36:*.oga=01;36:*.opus=01;36:*.spx=01;36:*.xspf=01;36:
 MAIL=/var/spool/mail/steinbusch1
-MANPATH=/p/software/jurecadc/stages/2022/software/binutils/2.37-GCCcore-11.2.0/share/man:/p/software/jurecadc/stages/2022/software/zlib/1.2.11-GCCcore-11.2.0/share/man:/p/software/jurecadc/stages/2022/software/GCCcore/11.2.0/share/man:/p/software/jurecadc/lmod/lmod/share/man:/usr/share/man:/usr/local/share/man:/opt/ddn/ime/share/man:/opt/ddn/ime/share/man:/opt/ddn/ime/share/man
+MANPATH=/p/software/jurecabooster/stages/2022/software/zlib/1.2.11-GCCcore-11.2.0/share/man:/p/software/jurecabooster/stages/2022/software/binutils/2.37-GCCcore-11.2.0/share/man:/p/software/jurecabooster/stages/2022/software/GCCcore/11.2.0/share/man:/p/software/jurecabooster/lmod/lmod/share/man:/p/software/jurecadc/stages/2022/software/binutils/2.37-GCCcore-11.2.0/share/man:/p/software/jurecadc/stages/2022/software/zlib/1.2.11-GCCcore-11.2.0/share/man:/p/software/jurecadc/stages/2022/software/GCCcore/11.2.0/share/man:/p/software/jurecadc/lmod/lmod/share/man:/usr/share/man:/usr/local/share/man:/opt/ddn/ime/share/man:/opt/ddn/ime/share/man:/opt/ddn/ime/share/man
 MODULEPATH=/p/software/jurecabooster/stages/2022/modules/all/Compiler/sidecompiler/GCCcore/11.2.0:/p/software/jurecabooster/stages/2022/modules/all/Compiler/GCCcore/11.2.0:/p/software/jurecabooster/stages/2022/UI/Defaults:/p/software/jurecabooster/stages/2022/UI/Tools:/p/software/jurecabooster/stages/2022/UI/Compilers:/p/software/jurecabooster/supercomputer_modules:/p/software/jurecabooster/productionstages:/p/software/jurecabooster/devel:/p/software/jurecabooster/userinstallations
 MODULEPATH_ROOT=/p/software/jurecabooster/stages/2022/modules/all
 MODULERCFILE=/p/software/jurecabooster/configs/modulerc.lua
 MODULESHOME=/p/software/jurecabooster/lmod/8.4.1
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-_ModuleTable005_=bnN0YWdlcyIsIi9wL3NvZnR3YXJlL2p1cmVjYWRjL2RldmVsIiwiL3Avc29mdHdhcmUvanVyZWNhZGMvdXNlcmluc3RhbGxhdGlvbnMiLH0sWyJzeXN0ZW1CYXNlTVBBVEgiXT0iL3Avc29mdHdhcmUvanVyZWNhZGMvc3VwZXJjb21wdXRlcl9tb2R1bGVzOi9wL3NvZnR3YXJlL2p1cmVjYWRjL3Byb2R1Y3Rpb25zdGFnZXM6L3Avc29mdHdhcmUvanVyZWNhZGMvZGV2ZWw6L3Avc29mdHdhcmUvanVyZWNhZGMvdXNlcmluc3RhbGxhdGlvbnMiLH0=
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 _ModuleTable_Sz_=5
 MPI_LOCALNRANKS=1
 MPI_LOCALRANKID=0
 OLDPWD=/p/home/jusers/steinbusch1/jureca
-OTHERSTAGES=/p/software/jurecadc/otherstages
-PATH=/p/home/jusers/steinbusch1/jureca/.cargo/bin:/p/home/jusers/steinbusch1/jureca/xenv/venv/bin:/p/home/jusers/steinbusch1/jureca/.cargo/bin:/p/home/jusers/steinbusch1/jureca/.cargo/bin:/p/software/jurecadc/stages/2022/software/binutils/2.37-GCCcore-11.2.0/bin:/p/software/jurecadc/stages/2022/software/GCCcore/11.2.0/bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/opt/ddn/ime/bin:/opt/jsc/bin:/usr/local/jsc/bin:/opt/parastation/bin:/p/software/jurecadc/bin:/opt/ddn/ime/bin:/opt/jsc/bin:/usr/local/jsc/bin:/opt/parastation/bin:/p/software/jurecadc/bin
+OTHERSTAGES=/p/software/jurecabooster/otherstages
+PATH=/p/software/jurecabooster/stages/2022/software/binutils/2.37-GCCcore-11.2.0/bin:/p/software/jurecabooster/stages/2022/software/GCCcore/11.2.0/bin:/p/home/jusers/steinbusch1/jureca/.cargo/bin:/p/home/jusers/steinbusch1/jureca/xenv/venv/bin:/p/home/jusers/steinbusch1/jureca/.cargo/bin:/p/home/jusers/steinbusch1/jureca/.cargo/bin:/p/software/jurecadc/stages/2022/software/binutils/2.37-GCCcore-11.2.0/bin:/p/software/jurecadc/stages/2022/software/GCCcore/11.2.0/bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/opt/ddn/ime/bin:/opt/jsc/bin:/usr/local/jsc/bin:/opt/parastation/bin:/p/software/jurecadc/bin:/opt/ddn/ime/bin:/opt/jsc/bin:/usr/local/jsc/bin:/opt/parastation/bin:/p/software/jurecadc/bin
 __PINNING__=00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000001
-PKG_CONFIG_PATH=/p/software/jurecadc/stages/2022/software/zlib/1.2.11-GCCcore-11.2.0/lib/pkgconfig
+PKG_CONFIG_PATH=/p/software/jurecabooster/stages/2022/software/zlib/1.2.11-GCCcore-11.2.0/lib/pkgconfig:/p/software/jurecadc/stages/2022/software/zlib/1.2.11-GCCcore-11.2.0/lib/pkgconfig
 PMI_APPNUM=0
 PMI_BARRIER_ROUNDS=10
 PMI_ENABLE_SOCKP=1
 PMI_FD=12
-PMI_ID=302659767
+PMI_ID=302664310
 PMI_RANK=0
 PMI_SIZE=1
 PMI_SUBVERSION=1
@@ -118,7 +118,7 @@
 PSI_APPNUM=0
 PSID_CPU_PINNING=0x00000000000000000000000000000000000000000000000000000000000000000001
 __PSID_USE_GPUS=
-__PSI_LOGGER_TID=302659767
+__PSI_LOGGER_TID=302664310
 PSI_NP_INFO=1
 PSI_USIZE_INFO=1
 PSP_DAPL=0
@@ -147,7 +147,7 @@
 SCRATCH_JSCbenchmark=/p/scratch/jscbenchmark
 SCRATCH_training2126=/p/scratch/training2126
 SHELL=/bin/bash
-SHLVL=2
+SHLVL=3
 SLURM_CLUSTER_NAME=jureca
 SLURM_CONF=/etc/slurm/slurm.conf
 SLURM_CPU_BIND_LIST=
@@ -163,8 +163,8 @@
 SLURM_JOB_CPUS_PER_NODE=272
 SLURM_JOB_CPUS_PER_NODE_PACK_GROUP_0=272
 SLURM_JOB_GID=4854
-SLURM_JOB_ID=10300143
-SLURM_JOBID=10300143
+SLURM_JOB_ID=10300259
+SLURM_JOBID=10300259
 SLURM_JOB_NAME=bash
 SLURM_JOB_NODELIST=jrc6618
 SLURM_JOB_NUM_NODES=1
@@ -195,23 +195,23 @@
 SLURM_SPANK_SLURM_SPANK_SET_NO_TURBOMODE=0
 SLURM_SPANK_START_CUDA_MPS=0
 SLURM_SRUN_COMM_HOST=10.14.0.42
-SLURM_SRUN_COMM_PORT=44303
-SLURM_STEP_ID=18
-SLURM_STEPID=18
-SLURM_STEP_LAUNCHER_PORT=44303
+SLURM_SRUN_COMM_PORT=43193
+SLURM_STEP_ID=0
+SLURM_STEPID=0
+SLURM_STEP_LAUNCHER_PORT=43193
 SLURM_STEP_NODELIST=jrc6618
 SLURM_STEP_NUM_NODES=1
 SLURM_STEP_NUM_TASKS=1
 SLURM_STEP_TASKS_PER_NODE=1
 SLURM_SUBMIT_DIR=/p/home/jusers/steinbusch1/jureca/xenv
 SLURM_SUBMIT_HOST=jrlogin01.jureca
-SLURM_TASK_PID=14533
+SLURM_TASK_PID=19076
 SLURM_TASKS_PER_NODE=1
 SLURM_WORKING_CLUSTER=jureca:10.14.0.35:6817:8960:109
-SOFTWAREROOT=/p/software/jurecadc
+SOFTWAREROOT=/p/software/jurecabooster
 SRUN_DEBUG=3
 STAGE=2022
-STAGES=/p/software/jurecadc/stages
+STAGES=/p/software/jurecabooster/stages
 SUDO_COMMAND=/bin/bash
 SUDO_GID=1025
 SUDO_UID=1115
@@ -223,4 +223,4 @@
 USER=steinbusch1
 VIRTUAL_ENV=/p/home/jusers/steinbusch1/jureca/xenv/venv
 which_declare=declare -f
-XDG_DATA_DIRS=/usr/local/share:/usr/share
+XDG_DATA_DIRS=/p/software/jurecabooster/stages/2022/software/zlib/1.2.11-GCCcore-11.2.0/share:/p/software/jurecabooster/stages/2022/software/binutils/2.37-GCCcore-11.2.0/share:/p/software/jurecabooster/stages/2022/software/GCCcore/11.2.0/share:/usr/local/share:/usr/share

The second commit completely replaces the existing environment with the environment that results from sourcing modules.sh rather than only updating variables modified by modules.sh. This is the diff to the environment due to the second commit:

--- xenv/new_env	2022-03-17 17:05:54.424112380 +0100
+++ xenv/newnew_env	2022-03-17 17:56:05.677025834 +0100
@@ -99,7 +99,7 @@
 PMI_BARRIER_ROUNDS=10
 PMI_ENABLE_SOCKP=1
 PMI_FD=12
-PMI_ID=302664310
+PMI_ID=302669236
 PMI_RANK=0
 PMI_SIZE=1
 PMI_SUBVERSION=1
@@ -113,12 +113,11 @@
 PROJECT_cparateam=/p/project/cparateam
 PROJECT_JSCbenchmark=/p/project/jscbenchmark
 PROJECT_training2126=/p/project/training2126
-PS1=(venv) [\u@\h \W]$ 
 __PSI_ALARM_TMOUT=120
 PSI_APPNUM=0
 PSID_CPU_PINNING=0x00000000000000000000000000000000000000000000000000000000000000000001
 __PSID_USE_GPUS=
-__PSI_LOGGER_TID=302664310
+__PSI_LOGGER_TID=302669236
 PSI_NP_INFO=1
 PSI_USIZE_INFO=1
 PSP_DAPL=0
@@ -163,8 +162,8 @@
 SLURM_JOB_CPUS_PER_NODE=272
 SLURM_JOB_CPUS_PER_NODE_PACK_GROUP_0=272
 SLURM_JOB_GID=4854
-SLURM_JOB_ID=10300259
-SLURM_JOBID=10300259
+SLURM_JOB_ID=10300307
+SLURM_JOBID=10300307
 SLURM_JOB_NAME=bash
 SLURM_JOB_NODELIST=jrc6618
 SLURM_JOB_NUM_NODES=1
@@ -195,17 +194,17 @@
 SLURM_SPANK_SLURM_SPANK_SET_NO_TURBOMODE=0
 SLURM_SPANK_START_CUDA_MPS=0
 SLURM_SRUN_COMM_HOST=10.14.0.42
-SLURM_SRUN_COMM_PORT=43193
-SLURM_STEP_ID=0
-SLURM_STEPID=0
-SLURM_STEP_LAUNCHER_PORT=43193
+SLURM_SRUN_COMM_PORT=44691
+SLURM_STEP_ID=2
+SLURM_STEPID=2
+SLURM_STEP_LAUNCHER_PORT=44691
 SLURM_STEP_NODELIST=jrc6618
 SLURM_STEP_NUM_NODES=1
 SLURM_STEP_NUM_TASKS=1
 SLURM_STEP_TASKS_PER_NODE=1
 SLURM_SUBMIT_DIR=/p/home/jusers/steinbusch1/jureca/xenv
 SLURM_SUBMIT_HOST=jrlogin01.jureca
-SLURM_TASK_PID=19076
+SLURM_TASK_PID=24002
 SLURM_TASKS_PER_NODE=1
 SLURM_WORKING_CLUSTER=jureca:10.14.0.35:6817:8960:109
 SOFTWAREROOT=/p/software/jurecabooster

See #6 (closed)

Edited by Benedikt Steinbusch

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