Changeset 1103 for palm

Timestamp:

Feb 20, 2013 2:15:53 AM (12 years ago)

Author:

raasch

Message:

small bugfixes; mrun and subjob scripts are made bash compatible; further adjustments for lckyuh

Location:

palm/trunk

Files:

• SCRIPTS/.mrun.config.hayaka (added)
• SCRIPTS/mrun (modified) (8 diffs)
• SCRIPTS/subjob (modified) (6 diffs)
• SOURCE/check_parameters.f90 (modified) (2 diffs)
• SOURCE/poisfft.f90 (modified) (8 diffs)

palm/trunk/SCRIPTS/mrun

@@ -1 @@
-#!/bin/bash 
+#!/bin/ksh 
 
 # mrun - script for running PALM jobs
@@ -22 +22 @@
 # Current revisions:
 # ------------------
-# 
+# default script runs again under ksh, because of unsolved problems with read
+# from stdin: when bash script is called from a ksh, message "read error: 0:
+# Resource temporarily unavailable" appears and script does not stop,
+# further bash compatibility adjustments,
+# shebang line replaced by /bin/bash when running jobs on lckyuh; no restarts
+# on lckyuh, but mrun does not terminate and issues a warning instead
 #
 # Former revisions:
@@ -151 +156 @@
  if [[ `hostname` = rte10 ]]
  then
-   return_addres=133.5.185.60
-   echo "+++ WARNING: fixed return_addres = $return_addres is used !!!!!"
+    return_addres=133.5.185.60
+    echo "+++ WARNING: fixed return_addres = $return_addres is used !!!!!"
  elif [[ `hostname` = climate0 ]]
  then
-   return_addres=165.132.26.68
-   echo "+++ WARNING: fixed return_addres = $return_addres is used !!!!!"
+    return_addres=165.132.26.68
+    echo "+++ WARNING: fixed return_addres = $return_addres is used !!!!!"
  elif [[ `hostname` = urban00 ]]
  then
-   return_addres=147.46.30.151
-   echo "+++ WARNING: fixed return_addres = $return_addres is used !!!!!"
+    return_addres=147.46.30.151
+    echo "+++ WARNING: fixed return_addres = $return_addres is used !!!!!"
  else
     return_addres=$(nslookup `hostname` 2>&1 | grep "Address:" | tail -1 | awk '{print $2}')
@@ -1494 +1499 @@
 
              # QUELLTEXT-DATEI DARF KEINE PFADE BEINHALTEN
-          if [[ $(print $filename | grep -c "/") != 0 ]]
+          if [[ $(echo $filename | grep -c "/") != 0 ]]
           then
              printf "\n  +++ source code file:  $filename"
@@ -2599 +2604 @@
     fi
  else
-    printf "\n\n  +++ skipping parameter file check due to following reason: $reason" 
+    printf "\n\n  +++ skipping parameter file check due to following reason: $reason \n" 
  fi
 
@@ -4577 +4582 @@
              then
                 ssh $SSH_PORTOPT $return_addres -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc " 
+             elif [[ $localhost = lckyuh ]]
+             then
+                printf "\n  +++ WARNING: no restart mechanism available for host \"$localhost\" "
+                printf "\n               please restart job manually using command:\n"
+                printf "\n               \"$mc\" "
              else
                 eval  $mc                # ' MUESSEN AUSGEWERTET WERDEN
@@ -4582 +4592 @@
              cd -  > /dev/null
           fi
-          printf "\n$striche\n  *** restart-run initiated \n"
+          if [[ $localhost = lckyuh ]]
+          then
+             printf "\n$striche\n  *** restart-run to be initiated manually\n"
+          else
+             printf "\n$striche\n  *** restart-run initiated \n"
+          fi
 
 
@@ -4801 +4816 @@
           # ABDECKZEICHEN VERHINDERN, DASS ERSETZUNGEN ERFOLGEN
        echo  "cat > $mrun_script_name <<\"%END%\""  >>  $jobfile
-       cat   ${PALM_BIN}/$mrun_script_name          >>  $jobfile
+       if [[ $host = lckyuh ]]
+       then
+          sed 's/\/bin\/ksh/\/bin\/bash/g' ${PALM_BIN}/$mrun_script_name  >>  $jobfile
+       else
+          cat  ${PALM_BIN}/$mrun_script_name        >>  $jobfile
+       fi
        echo  "%END%"                                >>  $jobfile
        echo  "chmod u+x $mrun_script_name"          >>  $jobfile

palm/trunk/SCRIPTS/subjob

@@ -23 +23 @@
 # Current revisions:
 # ------------------
-# 
+# bash compatibility adjustments (usage of OPTIND, output formatting with printf
+# instead typeset -L/R),
+# further adjustments for lckyuh
 #
 # Former revisions:
@@ -73 +75 @@
  typeset  -i   cputime=0  memory=0  Memory=0  minuten  resttime  sekunden  stunden
  typeset  -i   inumprocs  mpi_tasks=0  nodes=0  processes_per_node=0 tasks_per_node=0  threads_per_task=1
- typeset  -L20 spalte1
- typeset  -R40 spalte2
- typeset  -L60 spalte3
 
 
@@ -123 +122 @@
      (bd4)                   local_addres=130.73.232.67;  local_host=lcsgib;;
      (b01*|bicegate1)        local_addres=130.73.232.102; local_host=lcsgib;;
+     (b04*)                  local_addres=133.5.4.33;     local_host=lckyuh;;
      (bicegate2)             local_addres=130.73.232.103; local_host=lcsgib;;
      (blizzard1)             local_addres=136.172.40.15;  local_host=ibmh;;
@@ -220 +220 @@
 
     # JOBDATEINAMEN ALS NAECHSTES ARGUMENT HOLEN
- shift OPTIND-1; file_to_send=$1
+ (( to_shift = $OPTIND - 1 ))
+ shift $to_shift; file_to_send=$1
 
 
@@ -525 +526 @@
     printf "#--------------------------------------------------------------# \n"
     spalte1=SUBJOB;spalte2=$(date)
-    printf "| $spalte1$spalte2 | \n"
+    printf "| %-20s%40s | \n" "$spalte1" "$spalte2"
     printf "|                                                              | \n"
     printf "| values of parameters/options:                                | \n"
-    spalte1=local_host$punkte; spalte2=$punkte$local_host
-    printf "| $spalte1$spalte2 | \n"
-    spalte1=remote_host$punkte; spalte2=$punkte$remote_host
-    printf "| $spalte1$spalte2 | \n"
-    spalte1=queue$punkte; spalte2=$punkte$queue
-    printf "| $spalte1$spalte2 | \n"
-    spalte1=memory$punkte; spalte2="$punkte$memory mb"
-    printf "| $spalte1$spalte2 | \n"
-    spalte1=cputime$punkte; spalte2="$punkte$cputime sec"
-    printf "| $spalte1$spalte2 | \n"
-    spalte1=job_name$punkte; spalte2="$punkte$job_name"
-    printf "| $spalte1$spalte2 | \n"
+    spalte1=$(echo local_host$punkte | cut -c-20)
+    spalte2=$punkte$local_host
+    printf "| %-20s%40s | \n" "$spalte1" "${spalte2: -40}"
+    spalte1=$(echo remote_host$punkte | cut -c-20)
+    spalte2=$punkte$remote_host
+    printf "| %-20s%40s | \n" "$spalte1" "${spalte2: -40}"
+    spalte1=$(echo queue$punkte | cut -c-20)
+    spalte2=$punkte$queue
+    printf "| %-20s%40s | \n" "$spalte1" "${spalte2: -40}"
+    spalte1=$(echo memory$punkte | cut -c-20)
+    spalte2="$punkte$memory mb"
+    printf "| %-20s%40s | \n" "$spalte1" "${spalte2: -40}"
+    spalte1=$(echo cputime$punkte | cut -c-20)
+    spalte2="$punkte$cputime sec"
+    printf "| %-20s%40s | \n" "$spalte1" "${spalte2: -40}"
+    spalte1=$(echo job_name$punkte | cut -c-20)
+    spalte2="$punkte$job_name"
+    printf "| %-20s%40s | \n" "$spalte1" "${spalte2: -40}"
     printf "#--------------------------------------------------------------# \n\n"
 
@@ -1577 +1584 @@
        then
           chmod  u+x  $job_on_remhost
-          echo "$submcom  $job_on_remhost"
           eval  $submcom  $job_on_remhost
        elif [[ $local_host = nech ]]

palm/trunk/SOURCE/check_parameters.f90

@@ -20 +20 @@
 ! Current revisions:
 ! -----------------
-! 
+! Bugfix: turbulent inflow must not require cyclic fill in restart runs
 !
 ! Former revisions:
@@ -3436 +3436 @@
 !
 !-- Turbulent inflow requires that 3d arrays have been cyclically filled with
-!-- data from prerun
-    IF ( turbulent_inflow  .AND.  initializing_actions /= 'cyclic_fill' )  THEN
+!-- data from prerun in the first main run
+    IF ( turbulent_inflow  .AND.  initializing_actions /= 'cyclic_fill'  .AND. &
+         initializing_actions /= 'read_restart_data' )  THEN
        message_string = 'turbulent_inflow = .T. requires ' // &
                         'initializing_actions = ''cyclic_fill'' '

palm/trunk/SOURCE/poisfft.f90

@@ -20 +20 @@
 ! Current revisions:
 ! -----------------
-! 
+! tri, ar, and ar1 arguments in tridia-routines (2d) are removed because they
+! sometimes cause segmentation faults with intel 12.1 compiler
 !
 ! Former revisions:
@@ -370 +371 @@
        DO  j = nys_z, nyn_z
           IF ( j <= nnyh )  THEN
-             CALL maketri( tri, j )
+             CALL maketri( j )
           ELSE
-             CALL maketri( tri, ny+1-j )
+             CALL maketri( ny+1-j )
           ENDIF
-          CALL split( tri )
-          CALL substi( ar, ar1, tri, j )
+          CALL split
+          CALL substi( j )
        ENDDO
 !$OMP  END PARALLEL
@@ -381 +382 @@
 !
 !--    First y-level.
-       CALL maketri( tri, nys_z )
-       CALL split( tri )
-       CALL substi( ar, ar1, tri, 0 )
+       CALL maketri( nys_z )
+       CALL split
+       CALL substi( 0 )
 
 !
 !--    Further y-levels.
        DO  j = 1, nnyh - 1
-          CALL maketri( tri, j )
-          CALL split( tri )
-          CALL substi( ar, ar1, tri, j )
-          CALL substi( ar, ar1, tri, ny+1-j )
+          CALL maketri( j )
+          CALL split
+          CALL substi( j )
+          CALL substi( ny+1-j )
        ENDDO
-       CALL maketri( tri, nnyh )
-       CALL split( tri )
-       CALL substi( ar, ar1, tri, nnyh+nys )
+       CALL maketri( nnyh )
+       CALL split
+       CALL substi( nnyh+nys )
 #endif
 
     CONTAINS
 
-       SUBROUTINE maketri( tri, j )
+       SUBROUTINE maketri( j )
 
 !------------------------------------------------------------------------------!
@@ -416 +417 @@
           REAL    ::  a, c
           REAL    ::  ll(nxl_z:nxr_z)
-          REAL    ::  tri(5,nxl_z:nxr_z,0:nz-1)
 
 
@@ -476 +476 @@
 
 
-       SUBROUTINE substi( ar, ar1, tri, j )
+       SUBROUTINE substi( j )
 
 !------------------------------------------------------------------------------!
@@ -487 +487 @@
 
           INTEGER ::  i, j, k
-          REAL    ::  ar1(nxl_z:nxr_z,0:nz-1)
-          REAL    ::  tri(5,nxl_z:nxr_z,0:nz-1)
-#if defined( __parallel )
-          REAL    ::  ar(nxl_z:nxr_z,nys_z:nyn_z,1:nz)
-#else
-          REAL    ::  ar(1:nz,nys_z:nyn_z,nxl_z:nxr_z)
-#endif
 
 !
@@ -559 +552 @@
 
 
-       SUBROUTINE split( tri )
+       SUBROUTINE split
 
 !------------------------------------------------------------------------------!
@@ -568 +561 @@
 
           INTEGER ::  i, k
-          REAL    ::  tri(5,nxl_z:nxr_z,0:nz-1)
 
 !