EnvironmentModules/sample

• bsoft

  #%Module1.0
  set bsoft /apps/bsoft
  setenv BSOFT $bsoft
  setenv BPARAM $bsoft/parameters/
   
  prepend-path PATH $bsoft/bin
  prepend-path LD_LIBRARY_PATH $bsoft/lib

• ccp4-8

  #%Module1.0
  #
  puts stdout "source /apps/local/bin/ccp4-mkdir;"
  #
  set ccp4_master /apps
  set ccp4        $ccp4_master/ccp4-8.0
  set warp        $ccp4_master/arp_warp_8.0
  #
  setenv CCP4_MASTER $ccp4_master
  setenv CCP4        $ccp4
  setenv CBIN        $ccp4/bin
  setenv CLIB        $ccp4/lib
  setenv CLIBD       $ccp4/lib/data
  setenv CINCL       $ccp4/include
  setenv CETC        $ccp4/etc
  setenv CHTML       $ccp4/html
  setenv CEXAM       $ccp4/examples
  setenv CCP4I_TCLTK $ccp4/bin
  setenv CCP4_HELPDIR $ccp4/help/
  setenv CLIBD_MON   $ccp4/lib/data/monomers/
  setenv CCP4_OPEN   UNKNOWN
  setenv CCP4_SCR    /tmp/$env(USER)
   
  setenv CRANK       $ccp4/share/ccp4i/crank
  setenv CCP4I_TOP   $ccp4/share/ccp4i
   
  setenv warpbin     $warp/bin/bin-x86_64-Linux
  setenv warpdoc     $warp/manual
   
  setenv MMCIFDIC    $ccp4/lib/ccp4/cif_mmdic.lib
  setenv SSL_CERT_FILE $ccp4/etc/ssl/cacert.pem
   
  setenv BALBES_ROOT $ccp4/BALBES
   
  prepend-path PATH  $warp/bin/bin-x86_64-Linux:$ccp4/etc:$ccp4/bin
  prepend-path MANPATH $ccp4/share/man
   
  setenv GFORTRAN_UNBUFFERED_PRECONNECTED Y

• ccp4-7

  #%Module1.0
  #
  puts stdout "source /apps/local/bin/ccp4-mkdir;"
  #
  set ccp4_master /apps
  set ccp4        $ccp4_master/ccp4-7.0
  set warp        $ccp4_master/arp_warp_8.0
  #
  setenv CCP4_MASTER $ccp4_master
  setenv CCP4        $ccp4
  setenv CBIN        $ccp4/bin
  setenv CLIB        $ccp4/lib
  setenv CLIBD       $ccp4/lib/data
  setenv CINCL       $ccp4/include
  setenv CETC        $ccp4/etc
  setenv CHTML       $ccp4/html
  setenv CEXAM       $ccp4/examples
  setenv CCP4I_TCLTK $ccp4/bin
  setenv CCP4_HELPDIR $ccp4/help/
  setenv CLIBD_MON   $ccp4/lib/data/monomers/
  setenv CCP4_OPEN   UNKNOWN
  setenv CCP4_SCR    /tmp/$env(USER)
   
  setenv CRANK       $ccp4/share/ccp4i/crank
  setenv CCP4I_TOP   $ccp4/share/ccp4i
   
  setenv warpbin     $warp/bin/bin-x86_64-Linux
  setenv warpdoc     $warp/manual
   
  setenv MMCIFDIC    $ccp4/lib/ccp4/cif_mmdic.lib
  setenv SSL_CERT_FILE $ccp4/etc/ssl/cacert.pem
   
  prepend-path PATH  $warp/bin/bin-x86_64-Linux:$ccp4/etc:$ccp4/bin
  prepend-path MANPATH $ccp4/share/man
   
  setenv GFORTRAN_UNBUFFERED_PRECONNECTED Y

  /apps/local/bin/ccp4-mkdir

  #!/bin/bash
  if [ ! -d /tmp/$USER ]; then
     /bin/mkdir /tmp/$USER
  fi
  #あるいは
  /bin/rm -rf /tmp/$USER
  /bin/mkdir  /tmp/$USER

• ccpem

  #%Module1.0
   
  module load ccp4/8.0
   
  set ccpem /apps/ccpem-1.6.0
  setenv CCPEM $ccpem
   
  prepend-path PATH $ccpem/bin
  prepend-path LD_LIBRARY_PATH $ccpem/lib/modeller/install/lib/x86_64-intel8

• chimera

  #%Module1.0
  set-alias chimera /apps/chimera-1.15/bin/chimera

• cinderella

  #%Module
  set          root /apps/pyenv/versions/anaconda3-5.3.1/envs/cinderella
  prepend-path PATH $root/bin

• cisTEM

  #%Module1.0
  prepend-path PATH /apps/cistem-1.0.0-beta

• coot
  *PATH環境変数で定義するとcootのpythonが優勢になるので、エイリアスで対応

  #%Module1.0
  #
  set-alias coot /apps/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/bin/coot
  # ccpemのcoot 0.9-preなら
  # set-alias coot /apps/ccpem-1.5.0/bin/coot

• cryoDRGN

  #%Module -*- tcl -*-
  set          root /apps/pyenv/versions/anaconda3-5.3.1/envs/cryodrgn
  prepend-path PATH $root/bin

• crYOLO

  #%Module
  set          root       /apps/pyenv/versions/anaconda3-5.3.1/envs/cryolo
  setenv       CRYOLOPATH $root
  prepend-path PATH       $root/bin

• deepEMhancer

  #%Module1.0
  set          root /apps/pyenv/versions/anaconda3-5.3.1/envs/deepEMhancer_env/
  prepend-path PATH $root/bin

• EM2EM

  #%Module1.0
  set-alias em2em /apps/EM2EM/guiEM2EM.AppImage

• eman2.91
  「/etc/modulefiles/eman2/2.91」

  #%Module1.0
  set          EMAN2DIR        /apps/eman2.91
  setenv       EMAN2DIR        $EMAN2DIR
  prepend-path PATH            $EMAN2DIR/bin
  prepend-path LD_LIBRARY_PATH $EMAN2DIR/lib

• eman2.31

  #%Module1.0
  set          EMAN2DIR /apps/eman2.31
  setenv       EMAN2DIR $EMAN2DIR
  prepend-path PATH     $EMAN2DIR/bin

• eman2.12

  #%Module1.0
  set          EMAN2DIR   /apps/eman2.12
  setenv       EMAN2DIR   $EMAN2DIR
  prepend-path PATH       $EMAN2DIR/bin:$EMAN2DIR/extlib/bin
  prepend-path PYTHONPATH $EMAN2DIR/lib:$EMAN2DIR/bin

• EPU_group_AFIS

  #%Module1.0
  set          EPU_group_AFIS /apps/EPU_group_AFIS
  set          root           /apps/pyenv/versions/anaconda3-5.3.1/envs/EPU_group_AFIS
  prepend-path PATH           $EPU_group_AFIS:$root/bin

• Fiji

  #%Module1.0
  set-alias Fiji /apps/Fiji.app/ImageJ-linux64
  set-alias fiji /apps/Fiji.app/ImageJ-linux64

• Gautomatch

  #%Module1.0
  set-alias Gautomatch /apps/GCTF_Gautomatch_Cu10.1/Gautomatch_v0.56_sm30-75_cu10.1
  set-alias gautomatch /apps/GCTF_Gautomatch_Cu10.1/Gautomatch_v0.56_sm30-75_cu10.1

• Gctf

  #%Module1.0
  set-alias Gctf /apps/GCTF_Gautomatch_Cu10.1/GCTF_v1.18_sm30-75_cu10.1
  set-alias gctf /apps/GCTF_Gautomatch_Cu10.1/GCTF_v1.18_sm30-75_cu10.1

• IMOD

  #%Module1.0
  set imod     /apps/IMOD
  prepend-path PATH            $imod/bin
  prepend-path LD_LIBRARY_PATH $imod/lib
  prepend-path MANPATH         $imod/man
   
  setenv IMOD_DIR              $imod
  setenv IMOD_QTLIBDIR         $imod/qtlib
  setenv IMOD_PLUGIN_DIR       $imod/lib/imodplug
  #setenv IMOD_JAVADIR          /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.191.b12-1.el7_6.x86_64/jre/bin/
  setenv IMOD_JAVADIR          /usr
  setenv FOR_DISABLE_STACK_TRACE 1
  setenv IMOD_CALIB_DIR        $imod/autodoc
   
  set-alias subm "submfg \!* &"

  *「set-alias subm 'submfg \!* &'」でエラーになる場合があるので、素直に「source /apps/IMOD/IMOD-linux.sh」がいいかもしれない

• janni

  #%Module
  set          root /apps/pyenv/versions/anaconda3-5.3.1/envs/janni
  prepend-path PATH $root/bin

• MotionCor2

  #%Module
  set-alias MotionCor2 /apps/MotionCor2/MotionCor2_1.4.2_Cuda111-02-15-2020
  set-alias motioncor2 /apps/MotionCor2/MotionCor2_1.4.2_Cuda111-02-15-2020

• phenix

  #%Module1.0
  set phenix /apps/phenix-1.19.2-4158
  setenv PHENIX $phenix
  setenv PHENIX_VERSION 1.19.2-4158
  prepend-path PATH $phenix/build/bin

• PyEM

  #%Module1.0
  set PyEM /apps/PyEM/
  set root /apps/pyenv/versions/anaconda3-5.3.1/envs/PyEM
  prepend-path PATH $PyEM:$root/bin

• PyMOL

  #%Module1.0
  set pymol /apps/pymol
  set-alias pymol $pymol/bin/pymol
  #
  #「freeglut  ERROR:  Internal error <FBConfig with necessary capabilities not found> in function fgOpenWindow」が表示されるなら
  setenv LIBGL_ALWAYS_INDIRECT 1

• PyTom

  #%Module -*- tcl -*-
  set    root  /apps/pyenv/versions/anaconda3-5.3.1/envs/PyTom
  set    PYTOM /apps/pytom
  prepend-path PATH            $PYTOM/bin:$root/bin
  prepend-path LD_LIBRARY_PATH $PYTOM/external/lib
  prepend-path PYTHONPATH      $PYTOM

• relion-3.1.2

  #%Module1.0
  module load mpi
   
  set RELION /apps/relion-3.1.2
  prepend-path PATH            $RELION/bin
   
  setenv RELION_QSUB_COMMAND   qsub
  setenv RELION_MPIRUN         mpirun
  setenv RELION_QSUB_TEMPLATE  $RELION/bin/qsub.sh
  setenv RELION_QUEUE_NAME     s3
  setenv RELION_QUEUE_USE      false
   
  setenv RELION_QSUB_NRTHREADS         4
  setenv RELION_THREAD_MAX             16
  setenv RELION_QSUB_NRMPI             4
  setenv RELION_MPI_MAX                32
  setenv RELION_ERROR_LOCAL_MPI        32    #ローカルで32mpiより多く指定して計算するとエラー掲示
  setenv RELION_SHELL                  csh   # ctffindを外部コールに使用するSHELL
  setenv RELION_EXTERNAL_RECONSTRUCT_EXECUTABLE relion_external_reconstruct
   
  setenv RELION_CTFFIND_EXECUTABLE     /apps/ctffind-4.1.14/bin/ctffind
  setenv RELION_MOTIONCOR2_EXECUTABLE  /apps/MotionCor2/MotionCor2_1.4.2_Cuda111-02-15-2020
  setenv RELION_GCTF_EXECUTABLE        /apps/GCTF_Gautomatch_Cu10.1/GCTF_v1.18_sm30-75_cu10.1
  setenv RELION_RESMAP_EXECUTABLE      /apps/ResMap/ResMap-1.1.4-linux64
  setenv RELION_PDFVIEWER_EXECUTABLE   evince
  setenv RELION_SCRATCH_DIR            \$TMPDIR    # scratchの場所. pbsproのTMPDIRを使うなら
   
  setenv RELION_EXTERNAL_RECONSTRUCT_EXECUTABLE /apps/SIDESPLITTER/sidesplitter_wrapper.sh
  setenv SIDESPLITTER                           /apps/SIDESPLITTER/sidesplitter

• ResMap

  #%Module1.0
  set-alias ResMap /apps/ResMap/ResMap-1.1.4-linux64
  set-alias resmap /apps/ResMap/ResMap-1.1.4-linux64

• Scipion3

  #%Module1.0
  set-alias scipion3 /apps/scipion/scipion3

• SPRING

  #%Module1.0
  #
  prepend-path PATH /apps/spring_v0-86-1661/bin

• topaz

  #%Module1.0
  set          root /apps/pyenv/versions/anaconda3-5.3.1/envs/topaz
  prepend-path PATH $root/bin

• xds

  #%Module1.0
  prepend-path PATH /apps/xds

• xtal

  #%Module1.0
   
  prepend-path PATH /apps/xds:/apps/xds/xdsme/bin/noarch:/apps/xtal

cuda †

• cuda-12.1

  #%Module1.0
   
  set cuda /usr/local/cuda-12.1
   
  prepend-path PATH            $cuda/bin
  prepend-path LD_LIBRARY_PATH $cuda/lib64
  prepend-path MANPATH         $cuda/share/man

icc †

• icc

  #%Module1.0
  #
  set icc /opt/intel/compilers_and_libraries/linux
  set tbb $icc/tbb/lib/intel64/gcc4.7
  set mpi $icc/mpi/intel64/libfabric/lib:$icc/mpi/intel64/lib/releas:$icc/mpi/intel64/lib
  set mkl $icc/mkl/lib/intel64
  #
  setenv INTEL_LICENSE_FILE /opt/intel/licenses
  #
  setenv MKLROOT            $icc/mkl
  setenv TBBROOT            $icc/tbb
  setenv PSTLROOT           $icc/pstl
  setenv I_MPI_ROOT         $icc/mpi
  #
  setenv FI_PROVIDER        tcp
  setenv FI_PROVIDER_PATH   $icc/mpi/intel64/libfabric/lib/prov
  setenv CPATH              $icc/mkl/include:$icc/pstl/include:$icc/tbb/include
  setenv NLSPATH            $icc/lib/intel64/locale/%l_%t/%N:$icc/mkl/lib/intel64/locale/%l_%t/%N
   
  prepend-path PATH            $icc/bin/intel64:$icc/mpi/intel64/libfabric/bin:$icc/mpi/intel64/bin
  prepend-path LIBRARY_PATH    $icc/lib/intel64:$mpi:$mkl:$tbb  
  prepend-path LD_LIBRARY_PATH $icc/lib/intel64:$mpi:$mkl:$tbb  
  prepend-path MANPATH         /opt/intel/man/common:$icc/mpi/man
  prepend-path CLASSPATH       $icc/mpi/intel64/lib/mpi.jar
  prepend-path PKG_CONFIG_PATH $icc/mkl/bin/pkgconfig

• iccRuntime

  #%Module1.0
  #
  set icc /opt/intel/psxe_runtime_2019.4.243/linux
  set tbb $icc/tbb/lib/intel64/gcc4.7
  set mpi $icc/mpi/intel64/libfabric/lib:$icc/mpi/intel64/lib/release:$icc/mpi/intel64/lib
  set mkl $icc/mkl/lib/intel64
  set cmp $icc/compiler/lib/intel64_lin
  #
  setenv I_MPI_ROOT             $icc/mpi
  setenv FI_PROVIDER            tcp
  setenv FI_PROVIDER_PATH       $icc/mpi/intel64/libfabric/lib/prov
  #
  prepend-path PATH             $icc/mpi/intel64/libfabric/bin:$icc/mpi/intel64/bin
  prepend-path LIBRARY_PATH     $icc/mpi/intel64/libfabric/lib
  prepend-path LD_LIBRARY_PATH  $mpi:$mkl:$cmp:$tbb
  prepend-path MANPATH          $icc/mpi/man
  prepend-path CLASSPATH        $icc/mpi/intel64/lib/mpi.jar

• mklRuntime

  #%Module1.0
  #
  set icc /opt/intel/compilers_and_libraries_2020.2.254/linux
  #
  setenv INTEL_LICENSE_FILE $icc/licenses:/opt/intel/licenses
  #
  setenv MKLROOT            $icc/mkl
  setenv TBBROOT            $icc/tbb
  #
  setenv CPATH              $icc/mkl/include:$icc/tbb/include
  setenv NLSPATH            $icc/compiler/lib/intel64/locale/%l_%t/%N:$icc/mkl/lib/intel64_lin/locale/%l_%t/%N
  setenv LIBRARY_PATH       $icc/compiler/lib/intel64_lin:$icc/mkl/lib/intel64_lin:$icc/tbb/lib/intel64/gcc4.8
  #
  prepend-path PATH            $icc/bin/intel64:$icc/bin
  prepend-path LD_LIBRARY_PATH $icc/compiler/lib/intel64_lin:$icc/mkl/lib/intel64_lin:$icc/tbb/lib/intel64/gcc4.8
  prepend-path PKG_CONFIG_PATH $icc/mkl/bin/pkgconfig

• oneAPI

  #%Module1.0
  #
  set oneapi /opt/intel/oneapi
  #
  set icc           $oneapi/compiler/2021.4.0
  set icc-lib       $icc/linux/lib
  set icc-lib-ld    $icc-lib:$icc-lib/x64:$icc-lib/emu:$icc-lib/oclfpga/host/linux64/lib:$icc-lib/oclfpga/linux64/lib:$icc/linux/compiler/lib/intel64_lin
  set icc-bin       $icc/linux/lib/oclfpga/llvm/aocl-bin:$icc/linux/lib/oclfpga/bin:$icc/linux/bin/intel64:$icc/linux/bin
  set tbb           $oneapi/tbb/2021.4.0
  set mkl           $oneapi/mkl/2021.4.0
  set debugger      $oneapi/debugger/10.2.4
  set debugger-lib  $debugger/gdb/intel64/lib:$debugger/libipt/intel64/lib:$debugger/dep/lib
  set dev-utilities $oneapi/dev-utilities/2021.4.0
  #####################################################
  setenv ONEAPI_ROOT $oneapi
  setenv TBBROOT     $tbb
  setenv CMPLR_ROOT  $icc
  setenv MKLROOT     $mkl
  setenv INTELFPGAOCLSDKROOT $icc-lib/oclfpga
  setenv INTEL_PYTHONHOME $debugger/10.2.4/dep
  setenv GDB_INFO     $debugger/documentation/info/
  setenv INFOPATH    $debugger/gdb/intel64/lib
  setenv CMAKE_PREFIX_PATH $tbb
  setenv SETVARS_VARS_PATH $tbb/env/vars.sh
  setenv OCL_ICD_FILENAMES libintelocl_emu.so:libalteracl.so:$icc-lib/x64/libintelocl.so
  setenv FPGA_VARS_DIR  $icc-lib/oclfpga
  #####################################################
  prepend-path MANPATH         $debugger/documentation/en/man/common:$debugger
  prepend-path LIBRARY_PATH    $tbb/lib/intel64/gcc4.8:$mkl/lib/intel64:$icc/linux/compiler/lib/intel64_lin:$icc-lib
  prepend-path LD_LIBRARY_PATH $tbb/lib/intel64/gcc4.8:$mkl/lib/intel64:$debugger-lib:$icc-lib-ld
  prepend-path CPATH           $tbb/include:$mkl/include:$dev-utilities/include:$icc/linux/include
  prepend-path NLSPATH         $mkl/lib/intel64/locale/%l_%t/%N
  prepend-path PATH            $mkl/bin/intel64:$dev-utilities/bin:$debugger/gdb/intel64/bin:$icc-bin