Improve how the environment is sourced from modules.sh
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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_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