update patch for CRYSTAL

Author: Samuel Moors

easybuild/easyconfigs/c/CRYSTAL/CRYSTAL-23.1.0.1-gompi-2024a-Linux.eb

@@ -15,14 +15,14 @@ toolchain = {'name': 'gompi', 'version': '2024a'}
 
 sources = [
     f'utils{_ver[0]}.tar.gz',
-    f'%(namelower)s{_ver[0]}_v{"_".join(_ver[1:])}_Linux-ifort21.4_openmpi4.1.1_exe.tar.gz',
+    f'%(namelower)s{_ver[0]}_v{_ver[1]}_{_ver[2]}_{_ver[3]}_Linux-ifort21.4_openmpi4.1.1_exe.tar.gz',
 ]
 patches = ['%(name)s-%(version)s_fix_run_scripts.patch']
 checksums = [
     {'utils23.tar.gz': '6e45152e7a1561b89594257c5b1db126505aeaa0282e4ac09fc41e478a9db328'},
     {'crystal23_v1_0_1_Linux-ifort21.4_openmpi4.1.1_exe.tar.gz':
      'ded88a51a24f42aab3272d428dabf9ab8a1fa2621c95b7ee7f75632b59c7956b'},
-    {'CRYSTAL-23.1.0.1_fix_run_scripts.patch': '893a89450ef19a6f3b6b88129830f636c130de1ee3a813d62b044f24a1a5ab59'},
+    {'CRYSTAL-23.1.0.1_fix_run_scripts.patch': 'b2cae06e19c2cdec6eeb6b86d401ff0fd8c07180c48c8b18094262b3308ea21a'},
 ]
 
 download_instructions = f"{name} requires manual download from https://www.crystal.unito.it/"
@@ -54,9 +54,12 @@ sanity_check_paths = {
 modextravars = {
     'CRY23_UTILS': '%(installdir)s/bin',
     'CRY23_EXEDIR': '%(installdir)s/bin',
-    'MPIBIN': 'mpirun',  # change to your preferred MPI launcher
 }
 
 sanity_check_commands = _runscripts
 
+modluafooter = """
+setenv("CRY23_SCRDIR", pathJoin(os.getenv("VSC_SCRATCH"), "crystal_scrdir"))
+"""
+
 moduleclass = 'chem'

easybuild/easyconfigs/c/CRYSTAL/CRYSTAL-23.1.0.1_fix_run_scripts.patch

@@ -1,8 +1,9 @@
 Fix MPI in run scripts
 Author: Samuel Moors (Vrije Universiteit Brussel)
+
 diff -ur utils23.orig/runcry23 utils23/runcry23
---- utils23.orig/runcry23	2022-11-07 15:57:24.000000000 +0100
-+++ utils23/runcry23	2025-05-16 15:32:06.861320036 +0200
+--- utils23.orig/runcry23	2026-01-08 15:19:03.718122000 +0100
++++ utils23/runcry23	2026-01-08 17:35:54.349524000 +0100
 @@ -165,9 +165,6 @@
   set here = $PWD
   set TMPDIR = $CRY23_SCRDIR/tmp$$_`whoami`
@@ -23,24 +24,9 @@ diff -ur utils23.orig/runcry23 utils23/runcry23
   set OUTDIR  = $here
  #
 diff -ur utils23.orig/runMPPcry23 utils23/runMPPcry23
---- utils23.orig/runMPPcry23	2022-11-07 16:00:04.000000000 +0100
-+++ utils23/runMPPcry23	2025-05-16 15:41:33.528486399 +0200
-@@ -1,12 +1,10 @@
- #!/bin/csh -f
- ### CRYSTAL23 - running script for MPPcrystal executable 
-- if ( $#argv < 2) then
-+ if ( $#argv < 1) then
-   echo "  "
-   echo Usage: 
-   echo "  "
--  echo "$0" nproc inpfilename "["filename_restart_data "("r-filename")""]"
--  echo "  "
--  echo nproc  "                " number of processors to be used for the calculation
-+  echo "$0" inpfilename "["filename_restart_data "("r-filename")""]"
-   echo "  "
-   echo inpfilename.d12  "      " CRYSTAL input deck for wave function calculation
-   echo "  "
-@@ -177,9 +175,6 @@
+--- utils23.orig/runMPPcry23	2026-01-08 15:19:03.739398000 +0100
++++ utils23/runMPPcry23	2026-01-08 17:43:15.892592526 +0100
+@@ -177,9 +177,6 @@
   set here = $PWD
   set TMPDIR = $CRY23_SCRDIR/tmp_p$$_`whoami`
  #
@@ -50,7 +36,7 @@ diff -ur utils23.orig/runMPPcry23 utils23/runMPPcry23
   if (! $?CRY23_INP ) then
    set CRY23_INP = $here
   endif
-@@ -190,16 +185,13 @@
+@@ -190,11 +187,10 @@
    set OUTFILE = out
   endif
  #
@@ -60,17 +46,10 @@ diff -ur utils23.orig/runMPPcry23 utils23/runMPPcry23
   set OUTDIR  = $here
  # Note that the job launching line, later on, is custom too.
 - set MPIDIR   = /replace/this/line/with/your/own/mpibin/directory
-- set MPIBIN   = mpirun
+  set MPIBIN   = mpirun
  #
-- set NPROCS     = $1
-- set FILEPREFIX = $2
-- set F9PREFIX   = $3
-+ set FILEPREFIX = $1
-+ set F9PREFIX   = $2
- #
-  set OUTFILE="$FILEPREFIX".$OUTFILE
- #
-@@ -211,14 +203,6 @@
+  set NPROCS     = $1
+@@ -211,14 +207,6 @@
   echo output data in $OUTDIR/$OUTFILE >>& $OUTDIR/$OUTFILE
   echo output data in $OUTDIR/$OUTFILE
  #
@@ -85,7 +64,7 @@ diff -ur utils23.orig/runMPPcry23 utils23/runMPPcry23
  #
   if(-e $XDIR/MPPcrystal && ! -z $XDIR/MPPcrystal ) then
    echo MPPcrystal executable in $XDIR >>& $OUTDIR/$OUTFILE
-@@ -238,15 +222,6 @@
+@@ -238,15 +226,6 @@
    exit
   endif
  #
@@ -101,34 +80,19 @@ diff -ur utils23.orig/runMPPcry23 utils23/runMPPcry23
   if (-e $CRY23P_MACH/nodes.par && ! -z $CRY23P_MACH/nodes.par) then
    echo list of nodes in $CRY23P_MACH/nodes.par >>& $OUTDIR/$OUTFILE
    echo list of nodes in $CRY23P_MACH/nodes.par
-@@ -453,7 +428,7 @@
+@@ -453,7 +432,7 @@
  #
   echo MPPcrystal job running in $TMPDIR on each node ...
  # Job Launching line:
 - ${MPIDIR}/${MPIBIN} -machinefile $CRY23P_MACH/machines.LINUX -np $NPROCS $TMPDIR/MPPcrystal < $TMPDIR/INPUT >>& $OUTDIR/$OUTFILE
-+ ${MPIBIN} $TMPDIR/MPPcrystal < $TMPDIR/INPUT >>& $OUTDIR/$OUTFILE
++ ${MPIBIN} -np $NPROCS $TMPDIR/MPPcrystal < $TMPDIR/INPUT >>& $OUTDIR/$OUTFILE
   date >>& $OUTDIR/$OUTFILE
   echo Contents of temporary directory in master node `hostname`: >>& $OUTDIR/$OUTFILE
   ls -l >> $OUTDIR/$OUTFILE
 diff -ur utils23.orig/runPcry23 utils23/runPcry23
---- utils23.orig/runPcry23	2022-11-07 16:01:25.000000000 +0100
-+++ utils23/runPcry23	2025-05-16 15:32:22.316884285 +0200
-@@ -1,12 +1,10 @@
- #!/bin/csh -f
- ### CRYSTAL23 - running script for Pcrystal executable 
-- if ( $#argv < 2) then
-+ if ( $#argv < 1) then
-   echo "  "
-   echo Usage: 
-   echo "  "
--  echo "$0" nproc inpfilename "["filename_restart_data "("r-filename")""]"
--  echo "  "
--  echo nproc  "                " number of processors to be used for the calculation
-+  echo "$0" inpfilename "["filename_restart_data "("r-filename")""]"
-   echo "  "
-   echo inpfilename.d12  "      " CRYSTAL input deck for wave function calculation
-   echo "  "
-@@ -177,9 +175,6 @@
+--- utils23.orig/runPcry23	2026-01-08 15:19:03.783881000 +0100
++++ utils23/runPcry23	2026-01-08 17:42:44.381464880 +0100
+@@ -177,9 +177,6 @@
   set here = $PWD
   set TMPDIR = $CRY23_SCRDIR/tmp_p$$_`whoami`
  #
@@ -138,7 +102,7 @@ diff -ur utils23.orig/runPcry23 utils23/runPcry23
   if (! $?CRY23_INP ) then
    set CRY23_INP = $here
   endif
-@@ -190,17 +185,14 @@
+@@ -190,12 +187,11 @@
    set OUTFILE = out
   endif
  #
@@ -149,17 +113,10 @@ diff -ur utils23.orig/runPcry23 utils23/runPcry23
  # Note that the job launching line, later on, is custom too.
  # The next line defines a varable for the path to the MPI bin directory
 - set MPIDIR   = /replace/this/line/with/your/own/mpibin/directory
-- set MPIBIN   = mpirun
- #
-- set NPROCS     = $1
-- set FILEPREFIX = $2
-- set F9PREFIX   = $3
-+ set FILEPREFIX = $1
-+ set F9PREFIX   = $2
+  set MPIBIN   = mpirun
  #
-  set OUTFILE="$FILEPREFIX".$OUTFILE
- #
-@@ -212,14 +204,6 @@
+  set NPROCS     = $1
+@@ -212,14 +208,6 @@
   echo output data in $OUTDIR/$OUTFILE >>& $OUTDIR/$OUTFILE
   echo output data in $OUTDIR/$OUTFILE
  #
@@ -174,7 +131,7 @@ diff -ur utils23.orig/runPcry23 utils23/runPcry23
  #
   if(-e $XDIR/Pcrystal && ! -z $XDIR/Pcrystal ) then
    echo Pcrystal executable in $XDIR >>& $OUTDIR/$OUTFILE
-@@ -239,15 +223,6 @@
+@@ -239,15 +227,6 @@
    exit
   endif
  #
@@ -190,34 +147,19 @@ diff -ur utils23.orig/runPcry23 utils23/runPcry23
   if (-e $CRY23P_MACH/nodes.par && ! -z $CRY23P_MACH/nodes.par) then
    echo list of nodes in $CRY23P_MACH/nodes.par >>& $OUTDIR/$OUTFILE
    echo list of nodes in $CRY23P_MACH/nodes.par
-@@ -454,7 +429,7 @@
+@@ -454,7 +433,7 @@
  #
   echo Pcrystal job running in $TMPDIR on each node ...
  # Job Launching line:
 - ${MPIDIR}/${MPIBIN} -machinefile $CRY23P_MACH/machines.LINUX -np $NPROCS $TMPDIR/Pcrystal < $TMPDIR/INPUT >>& $OUTDIR/$OUTFILE
-+ ${MPIBIN} $TMPDIR/Pcrystal < $TMPDIR/INPUT >>& $OUTDIR/$OUTFILE
++ ${MPIBIN} -np $NPROCS $TMPDIR/Pcrystal < $TMPDIR/INPUT >>& $OUTDIR/$OUTFILE
   date >>& $OUTDIR/$OUTFILE
   echo Contents of temporary directory in master node `hostname`: >>& $OUTDIR/$OUTFILE
   ls -l >> $OUTDIR/$OUTFILE
 diff -ur utils23.orig/runPprop23 utils23/runPprop23
---- utils23.orig/runPprop23	2022-11-07 16:03:56.000000000 +0100
-+++ utils23/runPprop23	2025-05-16 16:15:06.555523261 +0200
-@@ -1,12 +1,10 @@
- #!/bin/csh -f
- ### CRYSTAL23 - running script for Pproperties executable 
-- if ( $#argv < 3) then
-+ if ( $#argv < 2) then
-   echo "  "
-   echo Usage: 
-   echo "  "
--  echo "$0" nproc inpfilename wavefuncfilename ""
--  echo "  "
--  echo nproc  "                " number of processors to be used for the calculation
-+  echo "$0" inpfilename wavefuncfilename ""
-   echo "  "
-   echo inpfilename.d3  "      " CRYSTAL input deck for wave function calculation
-   echo "  "
-@@ -113,7 +111,7 @@
+--- utils23.orig/runPprop23	2026-01-08 15:19:03.812290000 +0100
++++ utils23/runPprop23	2026-01-08 17:55:55.089408294 +0100
+@@ -113,7 +113,7 @@
    echo SEEBECK.DAT "  " inpfilename_wf-filename_SEEBECK.DAT "  " Seebeck coefficient "("BOLTZAO")"
    echo POWER.DAT "  " inpfilename_wf-filename_POWER.DAT "  " Power factor coefficient "("BOLTZAO")"
    echo KAPPA.DAT "    " inpfilename_wf-filename_KAPPA.DAT "    " electron thermal conductivity "("BOLTZAO")"
@@ -226,7 +168,7 @@ diff -ur utils23.orig/runPprop23 utils23/runPprop23
    echo TDF.DAT "      " inpfilename_wf-filename_TDF.DAT "      " transport distribution function "("BOLTZAO")"
  #
    echo definablename_numering_Kkindex_real.molden "     "definablename_numering_Kkindex_real.molden "    "data for Crystalline Orbitals Visualization "("ORBITALS")"
-@@ -196,9 +194,6 @@
+@@ -196,9 +196,6 @@
   set here = $PWD
   set TMPDIR = $CRY23_SCRDIR/tmp_p$$_`whoami`
  #
@@ -236,7 +178,7 @@ diff -ur utils23.orig/runPprop23 utils23/runPprop23
   if (! $?CRY23_INP ) then
    set CRY23_INP = $here
   endif
-@@ -209,16 +204,13 @@
+@@ -209,11 +206,10 @@
    set OUTFILE = outp
   endif
  #
@@ -246,17 +188,10 @@ diff -ur utils23.orig/runPprop23 utils23/runPprop23
   set OUTDIR  = $here
  # Note that the job launching line, later on, is custom too.
 - set MPIDIR   = /replace/this/line/with/your/own/mpibin/directory
-- set MPIBIN   = mpirun
- #
-- set NPROCS     = $1
-- set FILEPREFIX = $2
-- set F9PREFIX   = $3
-+ set FILEPREFIX = $1
-+ set F9PREFIX   = $2
+  set MPIBIN   = mpirun
  #
-  set OUTFILE="$FILEPREFIX".$OUTFILE
- #
-@@ -231,23 +223,6 @@
+  set NPROCS     = $1
+@@ -231,24 +227,6 @@
   echo output data in $OUTDIR/$OUTFILE >>& $OUTDIR/$OUTFILE
   echo output data in $OUTDIR/$OUTFILE
  #
@@ -277,21 +212,22 @@ diff -ur utils23.orig/runPprop23 utils23/runPprop23
 -  echo file machines.LINUX in $CRY23P_MACH not found or empty
 -  exit
 - endif
- #
+-#
   if (-e $CRY23P_MACH/nodes.par && ! -z $CRY23P_MACH/nodes.par) then
    echo list of nodes in $CRY23P_MACH/nodes.par >>& $OUTDIR/$OUTFILE
-@@ -340,7 +315,7 @@
+   echo list of nodes in $CRY23P_MACH/nodes.par
+@@ -340,7 +318,7 @@
     if (-e fort.9  && ! -z fort.9  ) then
     echo Pproperties job running in $TMPDIR ...
  # Job Launching line:
 -   ${MPIDIR}/${MPIBIN} -machinefile $CRY23P_MACH/machines.LINUX -np $NPROCS $TMPDIR/Pproperties < $TMPDIR/INPUT >>& $OUTDIR/$OUTFILE
-+   ${MPIBIN} $TMPDIR/Pproperties < $TMPDIR/INPUT >>& $OUTDIR/$OUTFILE
++   ${MPIBIN} -np $NPROCS $TMPDIR/Pproperties < $TMPDIR/INPUT >>& $OUTDIR/$OUTFILE
     date >>& $OUTDIR/$OUTFILE
      echo Contents of temporary directory: >>& $OUTDIR/$OUTFILE
      ls -l >>& $OUTDIR/$OUTFILE
 diff -ur utils23.orig/runprop23 utils23/runprop23
---- utils23.orig/runprop23	2022-11-07 16:05:11.000000000 +0100
-+++ utils23/runprop23	2025-05-16 16:10:42.492081970 +0200
+--- utils23.orig/runprop23	2026-01-08 15:19:03.844898000 +0100
++++ utils23/runprop23	2026-01-08 17:40:25.599611000 +0100
 @@ -89,7 +89,7 @@
    echo SEEBECK.DAT "  " inpfilename_wf-filename_SEEBECK.DAT "  " Seebeck coefficient "("BOLTZAO")"
    echo POWER.DAT "  " inpfilename_wf-filename_POWER.DAT "  " Power factor coefficient "("BOLTZAO")"