Changeset 892 for palm

Timestamp:

May 2, 2012 1:51:44 PM (12 years ago)

Author:

maronga

Message:

bugfixes in parameter file check, adapted for lcxe6 (was lcxt4), new mrun.config parameter %login_init_cmd introduced

Location:

palm/trunk

Files:

• SCRIPTS/.mrun.config.default (modified) (3 diffs, 1 prop)
• SCRIPTS/.mrun.config.forwind (modified) (5 diffs, 1 prop)
• SCRIPTS/.mrun.config.ibmh (modified) (2 diffs, 1 prop)
• SCRIPTS/.mrun.config.imuk (modified) (6 diffs, 1 prop)
• SCRIPTS/.mrun.config.imuk_hlrn (modified) (5 diffs, 1 prop)
• SCRIPTS/.mrun.config.imuk_ice2_netcdf4 (modified) (3 diffs, 1 prop)
• SCRIPTS/.mrun.config.lcxe6 (added)
• SCRIPTS/.mrun.config.lcxt4 (deleted)
• SCRIPTS/.mrun.config.riam (modified) (2 diffs, 1 prop)
• SCRIPTS/.mrun.config.yonsei2011 (modified) (2 diffs, 1 prop)
• SCRIPTS/mbuild (modified) (12 diffs)
• SCRIPTS/mrun (modified) (28 diffs)
• SCRIPTS/subjob (modified) (13 diffs)
• SOURCE/check_parameters.f90 (modified) (3 diffs)

palm/trunk/SCRIPTS/.mrun.config.default

@@ +1 @@
+#$Id$
 #column 1          column 2                                   column 3
 #name of variable  value of variable (~ must not be used)     scope
@@ -41 +42 @@
 # if you want this host to be used as a remote host, uncomment next line
 #%remote_username   <replace by your username on this host>      <hi> parallel
+# if you want to load modules on the remote host, use the following line
+#%modules           <replace by the modules to be loaded>        <hi> parallel
+# if you want to perform initial commands on ssh connections, use the following line
+#%login_init_cmd    <replace by the inital commands>             <hi> parallel
 #
 %write_binary                true                             restart
@@ -158 +163 @@
 PARTICLE_INFO     out:loc:tra  ptf       $base_data/$fname/MONITORING  _prt_info
 PARTICLE_DATA     out:loc:flpe prt#:prtf $base_data/$fname/OUTPUT      _prt_dat
-
+# A BLANK LINE MUST FOLLOW

palm/trunk/SCRIPTS/.mrun.config.forwind

@@ +1 @@
+#$Id$
 #column 1          column 2                                   column 3
 #name of variable  value of variable (~ must not be used)     scope
@@ -5 +6 @@
 %base_directory    $HOME/palm/current_version
 %base_data         $base_directory/JOBS
-%output_data       /data/work/fw/<user-id>/palm/current_version/JOBS
-# Replace <user-id> by your username on FLOW. Replace "/fw/" by "/iwes/" if
+%output_data       /data/work/fw/<replace by your username>/palm/current_version/JOBS
+# Replace <replace by your username> by your username on FLOW. Replace "/fw/" by "/iwes/" if
 # your user directory resides in /iwes/.
 %source_path       $base_directory/trunk/SOURCE
@@ -25 +26 @@
 # on host flow. Please note that other hosts may require different settings.
 #
-%remote_username   <user-id>                                      lcflow parallel
-%tmp_user_catalog  /data/work/fw/<user-id>/tmp                    lcflow parallel
-%tmp_data_catalog  /data/work/fw/<user-id>/palm_restart_data      lcflow parallel
-%compiler_name     mpiifort                                       lcflow parallel
-%compiler_name_ser ifort                                          lcflow parallel
+%remote_username   <replace by your username>                                      lcflow parallel
+%tmp_user_catalog  /data/work/fw/<replace by your username>/tmp                    lcflow parallel
+%tmp_data_catalog  /data/work/fw/<replace by your username>/palm_restart_data      lcflow parallel
+%compiler_name     mpiifort                                                        lcflow parallel
+%compiler_name_ser ifort                                                           lcflow parallel
 %cpp_options       -DMPI_REAL=MPI_DOUBLE_PRECISION:-DMPI_2REAL=MPI_2DOUBLE_PRECISION:-D__netcdf:-D__lc:-D__parallel  lcflow parallel
 %netcdf_inc        -I:/cm/shared/apps/netcdf/intel/64/4.1.3/include                 lcflow parallel
@@ -36 +37 @@
 %fopts             -xSSE4.2:-O3:-cpp:-r8:-align:all:-ftz:-fno-alias:-no-scalar-rep:-no-prec-div:-no-prec-sqrt:-ip:-nbs:-convert:little_endian   lcflow parallel
 %lopts             -xSSE4.2:-O3:-cpp:-r8:-align:all:-ftz:-fno-alias:-no-scalar-rep:-no-prec-div:-no-prec-sqrt:-ip:-nbs:-Vaxlib                  lcflow parallel
+%login_init_cmd    .:/cm/local/apps/environment-modules/3.2.6/Modules/3.2.6/init/bash\;:echo \$MODULEPATH\;:echo:\$MODULESHOME\;:MODULEPATH=/cm/shared/modulefiles/ lcflow parallel  lcflow parallel
+%modules           netcdf/intel/64/4.1.3:intel/ics/64/2011.0.013 intel/impi/64/4.0.1.007:hdf5/intel/64/1.8.7                                    lcflow parallel 
 #
 #
@@ -161 +164 @@
 PARTICLE_INFO     out:loc:tra  ptf       $base_data/$fname/MONITORING  _prt_info
 PARTICLE_DATA     out:loc:flpe prt#:prtf $base_data/$fname/OUTPUT      _prt_dat
-
+# A BLANK LINE MUST FOLLOW

palm/trunk/SCRIPTS/.mrun.config.ibmh

@@ +1 @@
+#$Id$
 #column 1          column 2                                   column 3
 #name of variable  value of variable (~ must not be used)     scope
@@ -147 +148 @@
 PARTICLE_INFO     out:loc:tra  ptf       $base_data/$fname/MONITORING  _prt_info
 PARTICLE_DATA     out:loc:flpe prt#:prtf $output_data/$fname/OUTPUT      _prt_dat
-
+# A BLANK LINE MUST FOLLOW

palm/trunk/SCRIPTS/.mrun.config.imuk

@@ -8 +8 @@
 %add_source_path   $base_directory/USER_CODE/$fname
 %depository_path   $base_directory/MAKE_DEPOSITORY
-%use_makefile      true
+#%use_makefile      true
 #
 # Enter your own host below by adding another line containing in the second
@@ -15 +15 @@
 # first characters of the host identifier should be "lc" (Linux cluster), "ibm"
 # (IBM-AIX), or "nec" (NEC-SX), respectively.
-%host_identifier   service100  lcsgih
-%host_identifier   r1*         lcsgih
-%host_identifier   h01*        lcsgih
-%host_identifier   r2*         lcsgib
-%host_identifier   b01*        lcsgib
-%host_identifier   gallego     lcmuk
-%host_identifier   nid00*      lcxt4
 #
-%remote_username   maronga     lcmuk parallel
-%tmp_user_catalog  /tmp                                          lcmuk parallel
-%compiler_name     mpif90                                        lcmuk parallel
-%compiler_name_ser ifort                                         lcmuk parallel
-%cpp_options       -D__mpi2:-DMPI_REAL=MPI_DOUBLE_PRECISION:-DMPI_2REAL=MPI_2DOUBLE_PRECISION:-D__netcdf:-D__netcdf_64bit   lcmuk parallel
-%netcdf_inc        -I:/muksoft_64/packages/netcdf/3.6.3/include            lcmuk parallel
-%netcdf_lib        -L/muksoft_64/packages/netcdf/3.6.3/lib:-lnetcdf        lcmuk parallel
-%fopts             -axW:-cpp:-r8:-nbs:-convert:little_endian:-I:/muksoft_64/packages/mpich2/2.1.0.5/include     lcmuk parallel
-%lopts             -axW:-cpp:-r8:-nbs:-Vaxlib:-L:/muksoft_64/packages/mpich2/2.1.0.5/lib                    lcmuk parallel
-#%hostfile          $base_directory/.hostfile                    lcmuk parallel
+%host_identifier   inferno      lcmuk
 #
-#%remote_username  maronga      lcmuk
-%tmp_user_catalog  /tmp                                          lcmuk
-%compiler_name     ifort                                         lcmuk
-%cpp_options       -D__netcdf:-D__netcdf_64bit                   lcmuk
-%netcdf_inc        -I:/muksoft_64/packages/netcdf/3.6.3/include       lcmuk
-%netcdf_lib        -L/muksoft_64/packages/netcdf/3.6.3/lib:-lnetcdf   lcmuk
-%fopts             -axW:-cpp:-r8:-nbs:-convert:little:endian     lcmuk
-%lopts             -axW:-cpp:-r8:-nbs:-Vaxlib                    lcmuk
+# version 02/05/2012
+%remote_username   <replace by your IMUK username>                             lcmuk
+#%tmp_user_catalog /home/<replace by your IMUK username>/palm/tmp/             lcmuk
+%compiler_name     ifort                                                       lcmuk
+%compiler_name_ser ifort                                                       lcmuk
+%cpp_options       -cpp:-D__netcdf                                             lcmuk
+%netcdf_inc        -I:/muksoft/packages/netcdf/3.6.3/include                   lcmuk
+%netcdf_lib        -L/muksoft/packages/netcdf/3.6.3/lib:-lnetcdf               lcmuk
+%mopts             -j:4                                                        lcmuk
+%fopts             -fltconsistency:-O3:-cpp:-r8:-nbs:-convert:little_endian    lcmuk
+%lopts             -fltconsistency:-O3:-cpp:-r8:-nbs:-Vaxlib                   lcmuk
 #
-%remote_username  maronga                                        lcmuk trace
-%tmp_user_catalog  /tmp                                          lcmuk trace
-%compiler_name     ifort                                         lcmuk trace
-%cpp_options       -D__netcdf:-D__netcdf_64bit                   lcmuk trace
-%netcdf_inc        -I:/muksoft_64/packages/netcdf/3.6.3/include       lcmuk trace
-%netcdf_lib        -L/muksoft_64/packages/netcdf/3.6.3/lib:-lnetcdf   lcmuk trace
-%fopts             -axW:-cpp:-g:-CB:-inline_debug_info:-r8:-nbs:-convert:little:endian     lcmuk trace
-%lopts             -axW:-cpp:-g:-CB:-inline_debug_info:-r8:-nbs:-Vaxlib                    lcmuk trace
+# version 02/05/2012
+%remote_username   <replace by your IMUK username>                             lcmuk parallel
+#%tmp_user_catalog /home/<replace by your IMUK username>/palm/tmp/             lcmuk parallel
+%compiler_name     mpif90                                                      lcmuk parallel
+%compiler_name_ser ifort                                                       lcmuk parallel
+%cpp_options       -cpp:-DMPI_REAL=MPI_DOUBLE_PRECISION:-DMPI_2REAL=MPI_2DOUBLE_PRECISION:-D__netcdf  lcmuk parallel
+%netcdf_inc        -I:/muksoft/packages/netcdf/3.6.3/include                   lcmuk parallel
+%netcdf_lib        -L/muksoft/packages/netcdf/3.6.3/lib:-lnetcdf               lcmuk parallel
+%mopts             -j:4                                                        lcmuk parallel
+%fopts             -axW:-O3:-cpp:-openmp:-r8:-fp-model:precise:-ftz:-fno-alias:-no-prec-div:-no-prec-sqrt:-ip:-nbs:-convert:little_endian  lcmuk parallel
+%lopts             -axW:-O3:-cpp:-openmp:-r8:-fp-model:precise:-ftz:-fno-alias:-no-prec-div:-no-prec-sqrt:-ip:-nbs:-Vaxlib                 lcmuk parallel
+#%hostfile          $base_directory/.hostfile                                  lcmuk parallel
 #
-%sgi_feature       ice                                        lcsgih parallel
-%remote_username   nikmaron                                   lcsgih parallel
-%compiler_name     mpif90                                     lcsgih parallel
-%compiler_name_ser ifort                                      lcsgih parallel
-%mpilib            mvapich2/1.2.0-intel                       lcsgih parallel
-%cpp_options       -DMPI_REAL=MPI_DOUBLE_PRECISION:-DMPI_2REAL=MPI_2DOUBLE_PRECISION:-D__netcdf:-D__netcdf_64bit   lcsgih parallel
-%netcdf_inc        -I:/sw/dataformats/netcdf/3.6.2/include    lcsgih parallel
-%netcdf_lib        -L/sw/dataformats/netcdf/3.6.2/lib:-lnetcdf:-lnetcdff      lcsgih parallel
-%fopts             -g:-w:-xT:-O3:-cpp:-r8:-ftz:-fno-alias:-no-prec-div:-no-prec-sqrt:-ip:-nbs:-convert:little_endian  lcsgih parallel
-%lopts             -g:-w:-xT:-O3:-cpp:-r8:-ftz:-fno-alias:-no-prec-div:-no-prec-sqrt:-ip:-nbs:-Vaxlib   lcsgih parallel
-#%tmp_data_catalog  /gfs1/work/nikmaron/palm_restart_data                             lcsgih parallel
-#%tmp_user_catalog  /gfs1/tmp/nikmaron                                                lcsgih parallel
-#
-%sgi_feature       ice                                        lcsgih parallel debug
-%remote_username   nikmaron                                   lcsgih parallel debug
-%totalview         true                                       lcsgih parallel debug
-%compiler_name     mpif90                                     lcsgih parallel debug
-%compiler_name_ser ifort                                      lcsgih parallel debug
-%mpilib            mvapich2/1.2.0-intel                       lcsgih parallel debug
-%cpp_options       -DMPI_REAL=MPI_DOUBLE_PRECISION:-DMPI_2REAL=MPI_2DOUBLE_PRECISION:-D__netcdf:-D__netcdf_64bit   lcsgih parallel debug
-%netcdf_inc        -I:/sw/dataformats/netcdf/3.6.2/include    lcsgih parallel debug
-%netcdf_lib        -L/sw/dataformats/netcdf/3.6.2/lib:-lnetcdf:-lnetcdff      lcsgih parallel debug
-%fopts             -C:-fpe0:-debug:-traceback:-g:-w:-xT:-O0:-cpp:-r8:-ftz:-fno-alias:-no-prec-div:-no-prec-sqrt:-ip:-nbs:-convert:little_endian  lcsgih parallel debug
-%lopts             -C:-fpe0:-debug:-traceback:-g:-w:-xT:-O0:-cpp:-r8:-ftz:-fno-alias:-no-prec-div:-no-prec-sqrt:-ip:-nbs:-Vaxlib           lcsgih parallel debug
-#%tmp_data_catalog  /gfs1/work/nikmaron/palm_restart_data      lcsgih parallel debug
-#%tmp_user_catalog  /gfs1/tmp/nikmaron                         lcsgih parallel debug
-#
-%sgi_feature       ice                                        lcsgib parallel
-%remote_username   nikmaron                                   lcsgib parallel
-%compiler_name     mpif90                                     lcsgib parallel
-%compiler_name_ser ifort                                      lcsgib parallel
-%mpilib            mvapich2/1.2.0-intel                       lcsgib parallel
-%cpp_options       -DMPI_REAL=MPI_DOUBLE_PRECISION:-DMPI_2REAL=MPI_2DOUBLE_PRECISION:-D__netcdf:-D__netcdf_64bit   lcsgib parallel
-%netcdf_inc        -I:/sw/dataformats/netcdf/3.6.2/include    lcsgib parallel
-%netcdf_lib        -L/sw/dataformats/netcdf/3.6.2/lib:-lnetcdf:-lnetcdff      lcsgib parallel
+# version 02/05/2012
+%remote_username   <replace by your IMUK username>                             lcmuk parallel trace
+#%tmp_user_catalog /home/<replace by your IMUK username>/palm/tmp/             lcmuk parallel trace
+%compiler_name     mpif90                                                      lcmuk parallel trace
+%compiler_name_ser ifort                                                       lcmuk parallel trace
+%cpp_options       -DMPI_REAL=MPI_DOUBLE_PRECISION:-DMPI_2REAL=MPI_2DOUBLE_PRECISION:-D__netcdf   lcmuk parallel trace
+%netcdf_inc        -I:/muksoft/packages/netcdf/3.6.3/include            lcmuk parallel trace
+%netcdf_lib        -L/muksoft/packages/netcdf/3.6.3/lib:-lnetcdf        lcmuk parallel trace
+%fopts             -C:-check:nooutput_conversion:-openmp:-fpe0:-debug:-traceback:-g:-w:-xT:-O0:-cpp:-r8:-ftz:-fno-alias:-no-prec-div:-no-prec-sqrt:-ip:-nbs:-convert:little_endian  lcmuk parallel trace
+%lopts             -C:-check:nooutput_conversion:-openmp:-fpe0:-debug:-traceback:-g:-w:-xT:-O0:-cpp:-r8:-ftz:-fno-alias:-no-prec-div:-no-prec-sqrt:-ip:-nbs:-Vaxlib                 lcmuk parallel trace
 
-%fopts             -g:-w:-xT:-O3:-cpp:-r8:-ftz:-fno-alias:-no-prec-div:-no-prec-sqrt:-ip:-nbs:-convert:little_endian  lcsgib parallel
-%lopts             -g:-w:-xT:-O3:-cpp:-r8:-ftz:-fno-alias:-no-prec-div:-no-prec-sqrt:-ip:-nbs:-Vaxlib   lcsgib parallel
-#%tmp_data_catalog  /gfs1/work/nikmaron/palm_restart_data                             lcsgib parallel
-#%tmp_user_catalog  /gfs1/tmp/nikmaron                                                lcsgib parallel
-#
-%sgi_feature       ice                                        lcsgib parallel debug
-%remote_username   nikmaron                                   lcsgib parallel debug
-%compiler_name     mpif90                                     lcsgib parallel debug
-%compiler_name_ser ifort                                      lcsgib parallel debug
-%mpilib            mvapich2/1.2.0-intel                       lcsgib parallel debug
-%cpp_options       -DMPI_REAL=MPI_DOUBLE_PRECISION:-DMPI_2REAL=MPI_2DOUBLE_PRECISION:-D__netcdf:-D__netcdf_64bit   lcsgib parallel debug
-%netcdf_inc        -I:/sw/dataformats/netcdf/3.6.2/include    lcsgib parallel debug
-%netcdf_lib        -L/sw/dataformats/netcdf/3.6.2/lib:-lnetcdf:-lnetcdff      lcsgib parallel debug
-%fopts             -C:-fpe0:-debug:-traceback:-g:-w:-xT:-O0:-cpp:-r8:-ftz:-fno-alias:-no-prec-div:-no-prec-sqrt:-ip:-nbs:-convert:little_endian  lcsgib parallel debug
-%lopts             -C:-fpe0:-debug:-traceback:-g:-w:-xT:-O0:-cpp:-r8:-ftz:-fno-alias:-no-prec-div:-no-prec-sqrt:-ip:-nbs:-Vaxlib           lcsgib parallel debug
-#%tmp_data_catalog  /gfs1/work/nikmaron/palm_restart_data      lcsgib parallel debug
-#%tmp_user_catalog  /gfs1/tmp/nikmaron                         lcsgib parallel debug
-
-#
-%remote_username     bjornm         lcxt4 parallel
-%tmp_user_catalog    /work/bjornm   lcxt4 parallel
-%tmp_data_catalog    /work/bjornm/PALM_RESTART_DATA  lcxt4 parallel
-#%job_catalog         /work/bjornm/job_queue lcxt4 parallel
-%compiler_name       ftn           lcxt4 parallel
-%compiler_name_ser   ftn           lcxt4 parallel
-%cpp_options        -DMPI_REAL=MPI_DOUBLE_PRECISION:-DMPI_2REAL=MPI_2DOUBLE_PRECISION:-D__netcdf:-D__intel_openmp_bug   lcxt4 parallel
-%netcdf_inc         -I/work/apps/netcdf-3.6.2-cnl-pgi/include      lcxt4 parallel
-%netcdf_lib         -L/work/apps/netcdf-3.6.2-cnl-pgi/lib:-lnetcdf lcxt4 parallel
-%fopts              -fastsse:-Mpreprocess:-r8:-Mnobackslash        lcxt4 parallel
-%lopts              -fastsse:-Mpreprocess:-r8:-Mnobackslash        lcxt4 parallel
-#%fopts              -Mbounds:-fastsse:-Mpreprocess:-r8:-Mnobackslash        lcxt4 parallel
-#%lopts              -Mbounds:-fastsse:-Mpreprocess:-r8:-Mnobackslash        lcxt4 parallel
-
-%email_notification  maronga@muk.uni-hannover.de                 lcxt4 parallel
-#
 %write_binary                true                             restart
 #
 #----------------------------------------------------------------------------
-# INPUT-commands, executed before running PALM - lines must start with "IC:" 
+# INPUT-commands, executed before running PALM - lines must start with "IC:"
 #----------------------------------------------------------------------------
 #IC:
@@ -146 +77 @@
 # Combine all particle information files
 OC:[[ -f PARTICLE_INFOS/_0000 ]]  &&  cat  PARTICLE_INFOS/* >> PARTICLE_INFO
-#
-# Collect plot data (2d/3d) into one file
-OC:combine_plot_fields.x
 #
 #----------------------------------------------------------------------------
@@ -182 +110 @@
 CPU_MEASURES      out:loc:tra  d3f     $base_data/$fname/MONITORING  _cpu
 #
-DATA_1D_PR_NETCDF    out:loc:tr   pr#:prf   $base_data/$fname/OUTPUT  _pr     nc
-#DATA_1D_PR_NETCDF    out:loc      pr#:prf   $base_data/$fname/OUTPUT  _pr     nc
-DATA_1D_SP_NETCDF    out:loc:tr   sp#:spf   $base_data/$fname/OUTPUT  _sp     nc
-DATA_1D_TS_NETCDF    out:loc:tr   ts#:tsf   $base_data/$fname/OUTPUT  _ts     nc
-DATA_1D_PTS_NETCDF   out:loc:tr   pts#:ptsf $base_data/$fname/OUTPUT  _pts    nc
-DATA_2D_XY_NETCDF    out:loc:tr   xy#:xyf   $base_data/$fname/OUTPUT  _xy     nc
-DATA_2D_XY_AV_NETCDF out:loc:tr   xy#:xyf   $base_data/$fname/OUTPUT  _xy_av  nc
-DATA_2D_XZ_NETCDF    out:loc:tr   xz#:xzf   $base_data/$fname/OUTPUT  _xz     nc
-DATA_2D_XZ_AV_NETCDF out:loc:tr   xz#:xzf   $base_data/$fname/OUTPUT  _xz_av  nc
-DATA_2D_YZ_NETCDF    out:loc:tr   yz#:yzf   $base_data/$fname/OUTPUT  _yz     nc
-DATA_2D_YZ_AV_NETCDF out:loc:tr   yz#:yzf   $base_data/$fname/OUTPUT  _yz_av  nc
-DATA_3D_NETCDF       out:loc:tr   3d#:3df   $base_data/$fname/OUTPUT  _3d     nc
-DATA_3D_AV_NETCDF    out:loc:tr   3d#:3df   $base_data/$fname/OUTPUT  _3d_av  nc
+DATA_1D_PR_NETCDF    out:loc:tr   pr#:prf   $base_data/$fname/OUTPUT  _pr      nc
+DATA_1D_SP_NETCDF    out:loc:tr   sp#:spf   $base_data/$fname/OUTPUT  _sp      nc
+DATA_1D_TS_NETCDF    out:loc:tr   ts#:tsf   $base_data/$fname/OUTPUT  _ts      nc
+DATA_1D_PTS_NETCDF   out:loc:tr   pts#:ptsf $base_data/$fname/OUTPUT  _pts     nc
+DATA_2D_XY_NETCDF    out:loc:tr   xy#:xyf   $base_data/$fname/OUTPUT  _xy      nc
+DATA_2D_XY_AV_NETCDF out:loc:tr   xy#:xyf   $base_data/$fname/OUTPUT  _xy_av   nc
+DATA_2D_XZ_NETCDF    out:loc:tr   xz#:xzf   $base_data/$fname/OUTPUT  _xz      nc
+DATA_2D_XZ_AV_NETCDF out:loc:tr   xz#:xzf   $base_data/$fname/OUTPUT  _xz_av   nc
+DATA_2D_YZ_NETCDF    out:loc:tr   yz#:yzf   $base_data/$fname/OUTPUT  _yz      nc
+DATA_2D_YZ_AV_NETCDF out:loc:tr   yz#:yzf   $base_data/$fname/OUTPUT  _yz_av   nc
+DATA_3D_NETCDF       out:loc:tr   3d#:3df   $base_data/$fname/OUTPUT  _3d      nc
+DATA_3D_AV_NETCDF    out:loc:tr   3d#:3df   $base_data/$fname/OUTPUT  _3d_av   nc
 DATA_MASK_01_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m01     nc
 DATA_MASK_01_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m01_av  nc
@@ -235 +162 @@
 DATA_MASK_20_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m20     nc
 DATA_MASK_20_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m20_av  nc
-DATA_PRT_NETCDF      out:loc:pe   prt#:prtf $base_data/$fname/OUTPUT  _prt    nc
-DATA_PRT_NETCDF      out:loc:trpe prt#:prtf $base_data/$fname/OUTPUT  _prt    nc
-DATA_DVR             out:loc:trpe dvr       $base_data/$fname/OUTPUT  _dvr 
+DATA_PRT_NETCDF      out:loc:pe   prt#:prtf $base_data/$fname/OUTPUT  _prt     nc
+DATA_PRT_NETCDF      out:loc:trpe prt#:prtf $base_data/$fname/OUTPUT  _prt     nc
+DATA_DVR             out:loc:trpe dvr       $base_data/$fname/OUTPUT  _dvr
 #
 DVRP_LOG          out:loc:tr   dv#       $base_data/$fname/MONITORING  _dvrp_log
@@ -244 +171 @@
 PARTICLE_INFO     out:loc:tra  ptf       $base_data/$fname/MONITORING  _prt_info
 PARTICLE_DATA     out:loc:flpe prt#:prtf $base_data/$fname/OUTPUT      _prt_dat
-
+# A BLANK LINE MUST FOLLOW

palm/trunk/SCRIPTS/.mrun.config.imuk_hlrn

@@ +1 @@
+#$Id$
 #column 1          column 2                                   column 3
 #name of variable  value of variable (~ must not be used)     scope
@@ -48 +49 @@
 %sgi_feature       ice2                                       lcsgih parallel
 %modules           intel.compiler/11.1.072:mpt:phdf5/1.8.5-mpt-intel-11.1:pnetcdf/4.1.1-mpt-intel-11.1  lcsgih parallel
+%login_init_cmd    .:/usr/share/modules/init/bash           lcsgih parallel
 #%remote_username    <replace by your HLRN username>          lcsgih parallel
 %compiler_name     ifort                                      lcsgih parallel
@@ -65 +67 @@
 %sgi_feature       ice2                                       lcsgih parallel trace
 %modules           intel.compiler/11.1.072:mpt:phdf5/1.8.5-mpt-intel-11.1:pnetcdf/4.1.1-mpt-intel-11.1  lcsgih parallel trace
+%login_init_cmd    .:/usr/share/modules/init/bash           lcsgih parallel trace
 #%remote_username    <replace by your HLRN username>          lcsgih parallel trace
 %compiler_name     ifort                                      lcsgih parallel trace
@@ -77 +80 @@
 #%tmp_data_catalog  /gfs2/work/<replace by your HLRN username>/palm_restart_data      lcsgih parallel trace
 #%tmp_user_catalog  /gfs2/tmp/<replace by your HLRN username>                         lcsgih parallel trace
+#
+#
+#
+%sgi_feature       ice2                                       lcsgib parallel
+%modules           intel.compiler/11.1.072:mpt:phdf5/1.8.5-mpt-intel-11.1:pnetcdf/4.1.1-mpt-intel-11.1  lcsgib parallel
+%login_init_cmd    .:/usr/share/modules/init/bash           lcsgib parallel
+#%remote_username    <replace by your HLRN username>          lcsgib parallel
+%compiler_name     ifort                                      lcsgib parallel
+%compiler_name_ser ifort                                      lcsgib parallel
+%cpp_options       -DMPI_REAL=MPI_DOUBLE_PRECISION:-DMPI_2REAL=MPI_2DOUBLE_PRECISION:-D__netcdf:-D__netcdf4:-D__mpi2   lcsgib parallel
+%netcdf_inc        -I:/sw/dataformats/pnetcdf/netcdf-4.1.1-mpt-intel-11.1/include:-I:/sw/dataformats/phdf5/hdf5-1.8.5-mpt-intel-11.1/include    lcsgib parallel
+%netcdf_lib        -L/sw/dataformats/pnetcdf/netcdf-4.1.1-mpt-intel-11.1/lib:-lnetcdf:-lnetcdff:-L/sw/dataformats/phdf5/hdf5-1.8.5-mpt-intel-11.1/lib:-lhdf5:-lhdf5_hl:-lz      lcsgib parallel
+%mopts             -j:4                                       lcsgib parallel
+%fopts             -openmp:-xS:-fpe0:-O3:-cpp:-r8:-fp-model:precise:-align:all:-ftz:-fno-alias:-no-scalar-rep:-no-prec-div:-no-prec-sqrt:-ip:-nbs:-convert:little_endian  lcsgib parallel
+%lopts             -openmp:-xS:-fpe0:-O3:-cpp:-r8:-fp-model:precise:-align:all:-ftz:-fno-alias:-no-scalar-rep:-no-prec-div:-no-prec-sqrt:-ip:-nbs:-Vaxlib:-lmpi           lcsgib parallel
+%memory            1500                                       lcsgib parallel
+#%tmp_data_catalog  /gfs2/work/<replace by your HLRN username>/palm_restart_data      lcsgib parallel
+#%tmp_user_catalog  /gfs2/tmp/<replace by your HLRN username>                         lcsgib parallel
+#
+#
+#
+%sgi_feature       ice2                                       lcsgib parallel trace
+%modules           intel.compiler/11.1.072:mpt:phdf5/1.8.5-mpt-intel-11.1:pnetcdf/4.1.1-mpt-intel-11.1  lcsgib parallel trace
+%login_init_cmd    .:/usr/share/modules/init/bash           lcsgib parallel trace
+#%remote_username    <replace by your HLRN username>          lcsgib parallel trace
+%compiler_name     ifort                                      lcsgib parallel trace
+%compiler_name_ser ifort                                      lcsgib parallel trace
+%cpp_options       -DMPI_REAL=MPI_DOUBLE_PRECISION:-DMPI_2REAL=MPI_2DOUBLE_PRECISION:-D__netcdf:-D__netcdf4:-D__mpi2   lcsgib parallel trace
+%netcdf_inc        -I:/sw/dataformats/pnetcdf/netcdf-4.1.1-mpt-intel-11.1/include:-I:/sw/dataformats/phdf5/hdf5-1.8.5-mpt-intel-11.1/include    lcsgib parallel trace
+%netcdf_lib        -L/sw/dataformats/pnetcdf/netcdf-4.1.1-mpt-intel-11.1/lib:-lnetcdf:-lnetcdff:-L/sw/dataformats/phdf5/hdf5-1.8.5-mpt-intel-11.1/lib:-lhdf5:-lhdf5_hl:-lz      lcsgib parallel trace
+%mopts             -j:4                                       lcsgib parallel trace
+%fopts             -openmp:-override-limits:-C:-ftrapuv:-xS:-debug:extended:-check:nooutput_conversion:-O0:-fpe0:-g:-traceback:-cpp:-r8:-fp-model:precise:-align:all:-ftz:-fno-alias:-no-scalar-rep:-no-prec-div:-no-prec-sqrt:-ip:-nbs:-convert:little_endian  lcsgib parallel trace
+%lopts             -openmp:-C:-ftrapuv:-xS:-debug:extended:-check:nooutput_conversion:-O0:-fpe0:-g:-traceback:-cpp:-r8:-fp-model:precise:-align:all:-ftz:-fno-alias:-no-scalar-rep:-no-prec-div:-no-prec-sqrt:-ip:-nbs:-Vaxlib:-lmpi           lcsgib parallel trace
+%memory            1500                                       lcsgib parallel trace
+#%tmp_data_catalog  /gfs2/work/<replace by your HLRN username>/palm_restart_data      lcsgib parallel trace
+#%tmp_user_catalog  /gfs2/tmp/<replace by your HLRN username>                         lcsgib parallel trace
 #
 #
@@ -156 +195 @@
 PARTICLE_INFO     out:loc:tra  ptf       $base_data/$fname/MONITORING  _prt_info
 PARTICLE_DATA     out:loc:flpe prt#:prtf $base_data/$fname/OUTPUT      _prt_dat
-
+# A BLANK LINE MUST FOLLOW

palm/trunk/SCRIPTS/.mrun.config.imuk_ice2_netcdf4

@@ +1 @@
+#$Id$
 #column 1          column 2                                   column 3
 #name of variable  value of variable (~ must not be used)     scope
@@ -47 +48 @@
 %sgi_feature       ice2                                       lcsgih parallel ice2
 %modules           intel.compiler:mvapich2:phdf5:pnetcdf      lcsgih parallel ice2
+%login_init_cmd    .:/usr/share/modules/init/bash           lcsgih parallel ice2
 #%remote_username  <replace by your HLRN username>            lcsgih parallel
 %compiler_name     mpif90                                     lcsgih parallel ice2
@@ -138 +140 @@
 PARTICLE_INFO     out:loc:tra  ptf       $base_data/$fname/MONITORING  _prt_info
 PARTICLE_DATA     out:loc:flpe prt#:prtf $base_data/$fname/OUTPUT      _prt_dat
-
+# A BLANK LINE MUST FOLLOW

palm/trunk/SCRIPTS/.mrun.config.riam

@@ +1 @@
+#$Id$
 #column 1          column 2                                   column 3
 #name of variable  value of variable (~ must not be used)     scope
@@ -165 +166 @@
 PARTICLE_INFO     out:loc:tra  ptf       $base_data/$fname/MONITORING  _prt_info
 PARTICLE_DATA     out:loc:flpe prt#:prtf $base_data/$fname/OUTPUT      _prt_dat
-
+# A BLANK LINE MUST FOLLOW

palm/trunk/SCRIPTS/.mrun.config.yonsei2011

@@ +1 @@
+#$Id$
 # recommended settings for Department of Atmospheric Sciences
 # machines climate0-climate3 (host identifier "lcyon")
@@ -206 +207 @@
 DATA_2D_YZ_NETCDF_O    out:loc:tr yzo#:yzof   $base_data/$fname/OUTPUT _o_yz  nc
 DATA_2D_YZ_AV_NETCDF_O out:loc:tr yzo#:yzof   $base_data/$fname/OUTPUT _o_yz_av  nc
+# A BLANK LINE MUST FOLLOW

palm/trunk/SCRIPTS/mbuild

@@ -130 +130 @@
      # 08/03/12 - BjornM- bugfix: cpp directive for namelist check program
      #                    corrected
-
+     # 02/05/12 - Bjoern  - lcxt4 is now lcxe6, adjustments for lcxe6, 
+     #                      bugfixes for the parameter file check, initial 
+     #                      commands on ssh calls sourced out to .mrun.config
 
 
@@ -511 +513 @@
         (lck)            remote_addres=165.132.26.61;;
         (lctit)          remote_addres=10.1.6.170;;
-        (lcxt4)          remote_addres=129.177.20.113;;
+        (lcxe6)          remote_addres=129.177.20.113;;
         (lcxt5m)         remote_addres=193.166.211.144;;
         (decalpha)       remote_addres=165.132.26.56;;
@@ -842 +844 @@
 
 
+       # get login init commands, "::" is replacing a space
+    line=""
+    grep  "$remote_host_string" $config_file | grep "%login_init_cmd"  >  $tmp_mbuild
+    while read line1
+    do
+
+       if [[ $(echo $line1 | cut -d" " -s -f3-) = "$remote_host_string" ]]
+       then
+          line="$line1"
+       fi
+
+       if [[ "$line" != ""  &&  $(echo $line | cut -c1) != "#" ]]
+       then
+             # EVENTUELLE DOPPELPUNKTE AUS DIREKTIVENSTRING ENTFERNEN
+          init_cmds=`echo $line | cut -d" " -s -f2 | sed 's/::/%DUM%/g' | sed 's/:/ /g' | sed 's/%DUM%/:/g'`
+       fi
+       init_cmds="${init_cmds};"
+    done < $tmp_mbuild
+
 
        # get modules to be loaded
@@ -861 +882 @@
 
     done < $tmp_mbuild
-
-
 
 
@@ -1011 +1030 @@
     if [[ $remote_host != $local_host ]]
     then
-
        if [[ $compile_utility_programs = false ]]
        then
@@ -1103 +1121 @@
           then
 
-             ssh  ${remote_username}@${remote_addres}  "$module_calls cd ${remote_md}; echo '$make_call_string' > LAST_MAKE_CALL; chmod u+x LAST_MAKE_CALL; $make_call_string; [[ \$? != 0 ]] && echo MAKE_ERROR" 2>&1 | tee ${remote_host}_last_make_protokoll
+             ssh  ${remote_username}@${remote_addres}  "$init_cmds $module_calls cd ${remote_md}; echo '$make_call_string' > LAST_MAKE_CALL; chmod u+x LAST_MAKE_CALL; $make_call_string; [[ \$? != 0 ]] && echo MAKE_ERROR" 2>&1 | tee ${remote_host}_last_make_protokoll
 
           elif [[ $remote_host = ibmh ]]
           then
 
-             print "$module_calls export OBJECT_MODE=64; cd ${remote_md}; echo $make_call_string > LAST_MAKE_CALL; chmod u+x LAST_MAKE_CALL; $make_call_string; [[ \$? != 0 ]] && echo MAKE_ERROR" | ssh  ${remote_username}@${remote_addres} 2>&1 | tee ${remote_host}_last_make_protokoll
+             print "$init_cmds $module_calls export OBJECT_MODE=64; cd ${remote_md}; echo $make_call_string > LAST_MAKE_CALL; chmod u+x LAST_MAKE_CALL; $make_call_string; [[ \$? != 0 ]] && echo MAKE_ERROR" | ssh  ${remote_username}@${remote_addres} 2>&1 | tee ${remote_host}_last_make_protokoll
 
           elif [[ $remote_host = lcsgib  ||  $remote_host = lcsgih ]]
           then
-
 #             print ". /usr/share/modules/init/bash; $module_calls  cd ${remote_md}; echo $make_call_string > LAST_MAKE_CALL; chmod u+x LAST_MAKE_CALL; $make_call_string; [[ \$? != 0 ]] && echo MAKE_ERROR" | ssh  ${remote_username}@${remote_addres} 2>&1 | tee ${remote_host}_last_make_protokoll
-             print "eval \`/sw/swdist/bin/modulesinit\`; $module_calls  cd ${remote_md}; echo $make_call_string > LAST_MAKE_CALL; chmod u+x LAST_MAKE_CALL; $make_call_string; [[ \$? != 0 ]] && echo MAKE_ERROR" | ssh  ${remote_username}@${remote_addres} 2>&1 | tee ${remote_host}_last_make_protokoll
+             print "$init_cmds $module_calls cd ${remote_md}; echo $make_call_string > LAST_MAKE_CALL; chmod u+x LAST_MAKE_CALL; $make_call_string; [[ \$? != 0 ]] && echo MAKE_ERROR" | ssh  ${remote_username}@${remote_addres} 2>&1 | tee ${remote_host}_last_make_protokoll
 
           elif [[ $remote_host = lctit ]]
@@ -1125 +1142 @@
              done
 
-          elif [[ $remote_host = lcxt4 ]]
-          then
-
-             ssh  ${remote_username}@${remote_addres} ". /opt/modules/default/init/ksh; $module_calls  cd ${remote_md}; echo $make_call_string > LAST_MAKE_CALL; chmod u+x LAST_MAKE_CALL; $make_call_string; [[ \$? != 0 ]] && echo MAKE_ERROR" 2>&1 | tee ${remote_host}_last_make_protokoll
-
-          else
-
-             print "cd $module_calls ${remote_md}; echo $make_call_string > LAST_MAKE_CALL; chmod u+x LAST_MAKE_CALL; $make_call_string; [[ \$? != 0 ]] && echo MAKE_ERROR" | ssh  ${remote_username}@${remote_addres} 2>&1 | tee ${remote_host}_last_make_protokoll
+          elif [[ $remote_host = lcxe6 ]]
+          then
+
+             ssh  ${remote_username}@${remote_addres} "$init_cmds $module_calls cd ${remote_md}; echo $make_call_string > LAST_MAKE_CALL; chmod u+x LAST_MAKE_CALL; $make_call_string; [[ \$? != 0 ]] && echo MAKE_ERROR" 2>&1 | tee ${remote_host}_last_make_protokoll
+
+          else
+
+             print "$init_cmds $module_calls cd ${remote_md}; echo $make_call_string > LAST_MAKE_CALL; chmod u+x LAST_MAKE_CALL; $make_call_string; [[ \$? != 0 ]] && echo MAKE_ERROR" | ssh  ${remote_username}@${remote_addres} 2>&1 | tee ${remote_host}_last_make_protokoll
 
           fi
@@ -1265 +1282 @@
           fi
 
+
           if [[ $remote_host = ibms  ||  $remote_host = ibmy ]]
           then
 
-             ssh  ${remote_username}@${remote_addres}  "$module_calls cd ${remote_ud}; $make_call_string; [[ \$? != 0 ]] && echo MAKE_ERROR"
+             ssh  ${remote_username}@${remote_addres}  "$init_cmds $module_calls cd ${remote_ud}; $make_call_string; [[ \$? != 0 ]] && echo MAKE_ERROR"
 
           elif [[ $remote_host = ibmh ]]
           then
 
-             print "$module_calls export OBJECT_MODE=64; cd ${remote_ud}; $make_call_string; [[ \$? != 0 ]] && echo MAKE_ERROR" | ssh  ${remote_username}@${remote_addres}
+             print "$init_cmds $module_calls export OBJECT_MODE=64; cd ${remote_ud}; $make_call_string; [[ \$? != 0 ]] && echo MAKE_ERROR" | ssh  ${remote_username}@${remote_addres}
 
           elif [[ $remote_host = lctit ]]
@@ -1281 +1299 @@
              while [[ $(cat ${remote_host}_last_make_protokoll | grep -c "Forwarding to N1GE") = 0 ]]
              do
-                print "$module_calls cd ${remote_ud}; $make_call_string; [[ \$? != 0 ]] && echo MAKE_ERROR" | ssh  ${remote_username}@${remote_addres} 2>&1 | tee ${remote_host}_last_make_protokoll
+                print "$init_cmds $module_calls cd ${remote_ud}; $make_call_string; [[ \$? != 0 ]] && echo MAKE_ERROR" | ssh  ${remote_username}@${remote_addres} 2>&1 | tee ${remote_host}_last_make_protokoll
              done
 
-          elif [[ $remote_host = lcxt4 ]]
-          then
-
-             ssh  ${remote_username}@${remote_addres} ". /opt/modules/default/init/ksh; $module_calls cd ${remote_ud}; $make_call_string; [[ \$? != 0 ]] && echo MAKE_ERROR" 2>&1 | tee ${remote_host}_last_make_protokoll
-
-          else
-
-             print "$module_calls cd ${remote_ud}; $make_call_string; [[ \$? != 0 ]] && echo MAKE_ERROR" | ssh  ${remote_username}@${remote_addres} 2>&1 | tee ${remote_host}_last_make_protokoll
+          elif [[ $remote_host = lcxe6 ]]
+          then
+
+             ssh  ${remote_username}@${remote_addres} "$init_cmds $module_calls cd ${remote_ud}; $make_call_string; [[ \$? != 0 ]] && echo MAKE_ERROR" 2>&1 | tee ${remote_host}_last_make_protokoll
+
+          else
+
+             print "$init_cmds $module_calls cd ${remote_ud}; $make_call_string; [[ \$? != 0 ]] && echo MAKE_ERROR" | ssh  ${remote_username}@${remote_addres} 2>&1 | tee ${remote_host}_last_make_protokoll
 
           fi
@@ -1302 +1320 @@
     else
 
-          # workaround for lcxt4
-       if [[ $remote_host = lcxt4 ]]
-       then
-          . /opt/modules/default/init/ksh
+          # workaround for lcxe6
+       if [[ $remote_host = lcxe6 ]]
+       then
+          $init_cmds
        fi
 
@@ -1415 +1433 @@
              echo "  *** compiling check_namelist_files ..."
 
+             # GET CHECK OPTIONS
+             line=""
+             found=false
+             grep  "$remote_host_string" $config_file | grep "%cpp_options"  >  $tmp_mbuild
+             while read line1
+             do
+
+                if [[ $(echo $line1 | cut -d" " -s -f3-) = "$remote_host_string" ]]
+                then
+                   line="$line1"
+                fi
+
+                if [[ "$line" != ""  &&  $(echo $line | cut -c1) != "#" ]]
+                then
+                   # EVENTUELLE DOPPELPUNKTE AUS OPTIONSSTRING UND ALLE -D ENTFERNEN
+                   line="$line "
+                   copts_check=`echo $line | cut -d" " -s -f2 | sed 's/::/%DUM%/g' | sed 's/:/ /g' | sed 's/%DUM%/:/g' | sed 's/-D[^ ]* //g' | sed 's/ -D.*//g'`
+                   found=true
+                fi
+
+             done < $tmp_mbuild
+             copts_check="$copts_check -D__check -D__parallel"
+
              check_depository_path=${local_source_path}/../UTIL
              cd $check_depository_path
@@ -1423 +1464 @@
              rm -rf ${mainprog}_sources_check.tar
 
-             copts_check="-cpp -D__parallel -D__check"
-             make  -f Makefile_check $make_options F90=$compiler_name_ser  COPT="$copts_check"
-
+             make  -f Makefile_check $make_options  F90=$compiler_name_ser  COPT="$copts_check"
              tar -cf  check_namelist_files.tar Makefile_check check_namelist_files.x *.f90 *.o *.mod
              mv check_namelist_files.tar $check_depository_path

palm/trunk/SCRIPTS/mrun

@@ -254 +254 @@
      # 12/03/12 - Siggi  - tasks_per_node divisor check not for lcflow
      # 21/03/12 - Matthias - default compiler on ibmh changed
+     # 02/05/12 - Bjoern  - lcxt4 is now lcxe6, adjustments for lcxe6, 
+     #                      bugfixes for the parameter file check, initial 
+     #                      commands on ssh calls sourced out to .mrun.config
 
 
@@ -333 +336 @@
  package_list=""
  punkte="..........................................................."
- p3d_suffix=""
  queue=none
  read_from_config=""
@@ -706 +708 @@
     do_remote=true
     case  $host  in
-        (ibm|ibmh|ibmkisti|ibmku|ibms|ibmy|nech|necriam|lckyoto|lcsgib|lcsgih|unics|lcxt4|lcxt5m|lck|lckordi)  true;;
+        (ibm|ibmh|ibmkisti|ibmku|ibms|ibmy|nech|necriam|lckyoto|lcsgib|lcsgih|unics|lcxe6|lcxt5m|lck|lckordi)  true;;
         (*)  printf "\n"
              printf "\n  +++ sorry: execution of batch jobs on remote host \"$host\""
@@ -870 +872 @@
                    do_remote=true
                    case  $host  in
-                       (ibm|ibmh|ibmkisti|ibmku|ibms|ibmy|lckyoto|lcsgib|lcsgih|nech|necriam|unics|lcxt4|lcxt5m|lck|lckordi)  true;;
+                       (ibm|ibmh|ibmkisti|ibmku|ibms|ibmy|lckyoto|lcsgib|lcsgih|nech|necriam|unics|lcxe6|lcxt5m|lck|lckordi)  true;;
                        (*)  printf "\n  +++ sorry: execution of batch jobs on remote host \"$host\""
                             printf "\n      is not available"
@@ -1154 +1156 @@
     do_remote=true
     case  $host  in
-        (ibm|ibmh|ibmkisti|ibmku|ibms|ibmy|lckyoto|lcsgib|lcsgih|nech|necriam|unics|lcxt4|lcxt5m|lck|lckordi)  true;;
+        (ibm|ibmh|ibmkisti|ibmku|ibms|ibmy|lckyoto|lcsgib|lcsgih|nech|necriam|unics|lcxe6|lcxt5m|lck|lckordi)  true;;
         (*)  printf "\n"
              printf "\n  +++ sorry: execution of batch jobs on remote host \"$host\""
@@ -1335 +1337 @@
        eval filename=${pathin[$i]}/${afname}${endin[$i]}
     fi
+    eval pathname=${pathin[$i]}
+
 
        # PRUEFEN AUF VORHANDENSEIN
@@ -2036 +2040 @@
  lopts="$lopts $netcdf_lib $dvr_lib"
  ROPTS="$ropts"
- if [[ ( $(echo $host | cut -c1-3) = nec  ||  $(echo $host | cut -c1-3) = ibm  ||  $host = lckyoto  ||  $host = lcsgih  ||  $host = lcsgib  ||  $host = lctit  ||  $host = lcfimm  ||  $host = lcxt4 ||  $host = lcxt5m || $host = lck || $host = lckordi)  &&  -n $numprocs ]]
+ if [[ ( $(echo $host | cut -c1-3) = nec  ||  $(echo $host | cut -c1-3) = ibm  ||  $host = lckyoto  ||  $host = lcsgih  ||  $host = lcsgib  ||  $host = lctit  ||  $host = lcfimm  ||  $host = lcxe6 ||  $host = lcxt5m || $host = lck || $host = lckordi)  &&  -n $numprocs ]]
  then
     XOPT="-X $numprocs"
@@ -2100 +2104 @@
     done
     mc="$mc -u$remote_username"
+ fi
+
+    # CHECK FOR INITIAL COMMANDS AFTER LOGIN
+ if [[ "$login_init_cmd" != "" ]]
+ then
+    export init_cmds="${login_init_cmd};"
  fi
 
@@ -2378 +2388 @@
  if [[ ! -f $check_depository/check_namelist_files.tar || ! -f $PALM_BIN/check_namelist_files.x ]]
  then
-    skip_check=true 
-
+      skip_check=true 
+      reason="parameter file check has not been compiled."
+ fi
+
+#CHECK FOR PARALLEL RUN; OTHERWISE SKIP CHECK
+ if [[ "$cond1" != "parallel"  &&  "$cond2" != "parallel" ]]
+ then
+     skip_check=true 
+     reason="serial run."
  fi
 
 #ONLY PERFORM CHECK IF -z OPTION IS NOT SET, NO RESTART RUN IS CARRIED OUT AND IF THE EXECUTION HOST IS THE LOCAL HOST
- if [[ $check_namelist_files == false || $fromhost != $localhost || $run_coupled_model == true || $restart_run == true ]]
+ if [[ $check_namelist_files == false ]]
+ then
+     skip_check=true
+     reason="-z option set."
+ fi
+
+ if [[ $fromhost != $localhost ]]
+ then
+     skip_check=true
+     reason="submitting host is local host."  
+ fi  
+
+ if [[ $run_coupled_model == true ]]
  then
     skip_check=true
- fi
+    reason="coupled run."  
+ fi
+
+ if [[ $restart_run == true ]]
+ then
+    skip_check=true
+    reason="restart run."     
+
+ fi
+
+#SKIP CHECK IN CASE OF RESTART RUN: CHECK WHETHER THE LAST CHAR IS "f" IN PARIN
+ ((last_char = `echo $filename | wc -c` - 1))
+ last_char=`echo $filename |cut -c$last_char`
+ if [[ "$last_char" == "f" ]]
+ then
+    skip_check=true
+    reason="restart run.)"
+ fi 
+
  if [[ $skip_check == false ]]
  then
-    if [[ $ocean_file_appendix == true ]]
-    then
-       d3par_string="d3o#"
-       d3fpar_string="d3of"
-    else
-       d3par_string="d3#"
-       d3fpar_string="d3f"
-    fi
 
     tmp_check=${working_directory}/tmp_check
 
-#   GET PARAMETER FILE SUFFIX (USUALLY "_P3D")
+#   GET TOPOGRAPHY PARAMETER FILE SUFFIX (USUALLY "_P3DF"). THIS FILE MIGHT IS
+#   NOT NECESSARILY REQUIRED
     line=""
     found=false
-    grep  "$d3par_string" $config_file | grep "PARIN"  >  $tmp_check
+    grep  "TOPOGRAPHY_DATA" $config_file  >  $tmp_check
     while read line1
     do
@@ -2409 +2449 @@
        if [[ "$line" != ""  &&  $(echo $line | cut -c1) != "#" ]]
        then
-             # EVENTUELLE DOPPELPUNKTE AUS OPTIONSSTRING ENTFERNEN
-          p3d_suffix=`echo $line | tr -s " " | cut -d" " -s -f5`
-          found=true
-       fi
-    done < $tmp_check
-
-    if [[ $found = false ]]
-    then
-       printf "\n  +++ no PARIN list entry found for $d3par_string in the configuration file."
-
-       locat=check_namelist; exit
-    fi
-
-#   GET RESTART PARAMETER FILE SUFFIX (USUALLY "_P3DF"). THIS FILE MIGHT IS
-#   NOT NECESSARILY REQUIRED
-    line=""
-    found=false
-    grep  "d3f" $config_file | grep "PARIN"  >  $tmp_check
-    while read line1
-    do
-       line="$line1"
-       if [[ "$line" != ""  &&  $(echo $line | cut -c1) != "#" ]]
-       then
-          p3df_suffix=`echo $line | tr -s " " | cut -d" " -s -f5`
-          found=true
-       fi
-    done < $tmp_check
-
-    if [[ $found = false ]]
-    then
-       printf "\n  +++ no PARIN list entry found for d3f in the configuration file."
-    fi
-
-#   GET TOPOGRAPHY PARAMETER FILE SUFFIX (USUALLY "_P3DF"). THIS FILE MIGHT IS
-#   NOT NECESSARILY REQUIRED
-    line=""
-    found=false
-    grep  "d3f" $config_file | grep "TOPOGRAPHY_DATA"  >  $tmp_check
-    while read line1
-    do
-       line="$line1"
-       if [[ "$line" != ""  &&  $(echo $line | cut -c1) != "#" ]]
-       then
           topo_suffix=`echo $line | tr -s " " | cut -d" " -s -f5`
           found=true
@@ -2467 +2464 @@
     for  item  in  $input_list
     do
-       if [[ "$item" == "restart" || "$item" == d3f || "$item" == d3of ]]
+       if [[ "$item" == "restart" ]]
        then
           check_restart=1
@@ -2476 +2473 @@
 
 #   ERROR IF NO PARAMETER FILE WAS FOUND, OTHERWISE PROCEED
-    if [[ ! -f $working_directory/JOBS/$fname/INPUT/${fname}${p3d_suffix} ]]
-    then
-       printf "\n\n  +++ ERROR: parameter file (${fname}${p3d_suffix}) not found." 
+    if [[ ! -f $filename ]]
+    then
+       printf "\n\n  +++ ERROR: parameter file ($filename) not found." 
        locat=check_namelist; exit
     fi
@@ -2485 +2482 @@
     if  [[ $check_restart == 1 ]]
     then
-       if [[ ! -f $working_directory/JOBS/$fname/INPUT/${fname}${p3df_suffix} ]]
-       then
-          printf "\n\n  +++ WARNING: restart parameter file (${fname}${p3df_suffix}) is missing."  
+
+
+
+       filenamef="${filename}f"
+       if [[ ! -f $filenamef ]]
+       then
+          printf "\n\n  +++ WARNING: restart parameter file ($filenamef) is missing."  
           check_restart=0
           answer=dummy
@@ -2514 +2515 @@
     cd $check_sources
 
+
 #   CHECK FOR USER CODE, OTHERWISE USE THE PRECOMPILED CHECK_NAMELIST_FILES.X
-    if [[ -d $working_directory/USER_CODE/$fname ]]
+    if [[ -d $add_source_path ]]
     then
        printf "\n\n  *** copying files from $check_depository" 
@@ -2524 +2526 @@
 
        printf "\n\n  *** adding user code." 
-       cp $working_directory/USER_CODE/$fname/* ./
+       cp $add_source_path/* ./
        touch check_namelist_files.f90
 
@@ -2561 +2563 @@
     fi
 
-    cp $working_directory/JOBS/$fname/INPUT/${fname}${p3d_suffix} ./PARIN
+    cp $filename ./PARIN
     if [[ $check_restart == 1 ]] 
     then
-       cp $working_directory/JOBS/$fname/INPUT/${fname}${p3df_suffix} ./PARINF   
-    fi
-
-
-    if [[ -f $working_directory/JOBS/$fname/INPUT/${fname}${topo_suffix} && $skip_check == false ]]
+       cp $filenamef ./PARINF   
+    fi
+
+cat ${pathname}/${fname}${topo_suffix}
+    if [[ -f ${pathname}/${fname}${topo_suffix} && $skip_check == false ]]
     then
        printf "\n  *** adding topography data"
-       cp $working_directory/JOBS/$fname/INPUT/${fname}${topo_suffix} ./TOPOGRAPHY_DATA
+       cp ${pathname}/${fname}${topo_suffix} ./TOPOGRAPHY_DATA
 
 #      IN CASE OF TOPOGRAPHY AND HIGH GRID POINT NUMBERS, THE STACK SIZE 
@@ -2620 +2622 @@
 
 #      CHECKING THE P3D FILE
-       printf "\n\n      (1) checking $fname$p3d_suffix"  
+       printf "\n\n      (1) checking $filename"  
        echo "$numprocs 0" > VARIN
        errors=`./check_namelist_files.x < VARIN 2>&1`
@@ -2637 +2639 @@
        if [[ $check_restart == 1 && $check_error == false ]]
        then
-          printf "\n\n      (2) checking $fname$p3df_suffix"  
+          printf "\n\n      (2) checking $filenamef"  
 
 #         FIRST CHECK IF INITIALIZING_ACTIONS="READ_RESTART_DATA" IS SET IN &INIPAR LIST
@@ -2711 +2713 @@
     fi
  else
-    printf "\n\n  +++ skipping parameter file check\n" 
+    printf "\n\n  +++ skipping parameter file check due to following reason: $reason" 
  fi
 
@@ -2717 +2719 @@
  rm -rf  $check_sources
  cd $working_directory
+
 
     # FALLS AUF DIESER MASCHINE GERECHNET WERDEN SOLL, WERDEN JETZT ENTSPRE-
@@ -2876 +2879 @@
        if [[ $localhost = nech ]]
        then
-          ssh  136.172.44.192 -l $usern ". /SX/opt/etc/initsx.sh; $module_calls cd \$HOME/work/${usern}.$kennung; sxmake $mopts -f Makefile PROG=a.out  F90=$compiler_name  COPT=\"$cpp_options\"  F90FLAGS=\"$fopts\"  LDFLAGS=\"$lopts\" "
+#         init_cmds was ". /SX/opt/etc/initsx.sh;" 
+          ssh  136.172.44.192 -l $usern "$init_cmds $module_calls cd \$HOME/work/${usern}.$kennung; sxmake $mopts -f Makefile PROG=a.out  F90=$compiler_name  COPT=\"$cpp_options\"  F90FLAGS=\"$fopts\"  LDFLAGS=\"$lopts\" "
           cp  $TEMPDIR_COMPILE/a.out  .
           [[ $? != 0 ]]  &&  compile_error=true
@@ -2883 +2887 @@
        then
           printf "      compiler is called via ssh on \"plogin1\" \n"
-          ssh  plogin1  -l $usern  "export PATH=/sw/ibm/xlf/13.1.0.8/usr/bin:$PATH; $module_calls cd $TEMPDIR; make $mopts -f Makefile PROG=a.out  F90=$compiler_name  COPT=\"$cpp_options\"  F90FLAGS=\"$fopts\"  LDFLAGS=\"$lopts\" "
+          ssh  plogin1  -l $usern  "$init_cmds export PATH=/sw/ibm/xlf/13.1.0.8/usr/bin:$PATH; $module_calls cd $TEMPDIR; make $mopts -f Makefile PROG=a.out  F90=$compiler_name  COPT=\"$cpp_options\"  F90FLAGS=\"$fopts\"  LDFLAGS=\"$lopts\" "
           [[ ! -f a.out ]]  &&  compile_error=true
           continue   # ANDERENFALLS IST STATUS=1, FALLS A.OUT VORHANDEN
@@ -2889 +2893 @@
        then
           printf "      compiler is called via ssh on \"bicegate0\" \n"
-          ssh  bicegate0  -l $usern  ". /usr/share/modules/init/bash; $module_calls cd $TEMPDIR; make $mopts -f Makefile PROG=a.out  F90=$compiler_name  COPT=\"$cpp_options\"  F90FLAGS=\"$fopts\"  LDFLAGS=\"$lopts\" "
+          ssh  bicegate0  -l $usern  "$init_cmds $module_calls cd $TEMPDIR; make $mopts -f Makefile PROG=a.out  F90=$compiler_name  COPT=\"$cpp_options\"  F90FLAGS=\"$fopts\"  LDFLAGS=\"$lopts\" "
           [[ ! -f a.out ]]  &&  compile_error=true
           continue   # ANDERENFALLS IST STATUS=1, FALLS A.OUT VORHANDEN
@@ -2895 +2899 @@
        then
           printf "      compiler is called via ssh on \"hicegate0\" \n"
-          ssh  hicegate0    -l $usern  ". /usr/share/modules/init/bash; $module_calls cd $TEMPDIR; make $mopts -f Makefile PROG=a.out  F90=$compiler_name  COPT=\"$cpp_options\"  F90FLAGS=\"$fopts\"  LDFLAGS=\"$lopts\" 2>&1 "
+          ssh  hicegate0  -l $usern  "$init_cmds $module_calls cd $TEMPDIR; make $mopts -f Makefile PROG=a.out  F90=$compiler_name  COPT=\"$cpp_options\"  F90FLAGS=\"$fopts\"  LDFLAGS=\"$lopts\" 2>&1 "
           [[ ! -f a.out ]]  &&  compile_error=true
           continue   # ANDERENFALLS IST STATUS=1, FALLS A.OUT VORHANDEN
@@ -2901 +2905 @@
        then 
           printf "      compiler is called via ssh on \"flow\" \n"
-          ssh  flow02.hpc.uni-oldenburg.de -l $usern ". /cm/local/apps/environment-modules/3.2.6/Modules/3.2.6/init/bash; echo $MODULEPATH; echo $MODULESHOME; MODULEPATH=/cm/shared/modulefiles/; module load netcdf/intel/64/4.1.3 intel/ics/64/2011.0.013 intel/impi/64/4.0.1.007 hdf5/intel/64/1.8.7; cd $TEMPDIR; make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT=\"$cpp_options\" F90FLAGS=\"$fopts\" LDFLAGS=\"$lopts\" "
+          ssh  flow02.hpc.uni-oldenburg.de -l $usern "$init_cmds $module_calls cd $TEMPDIR; make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT=\"$cpp_options\" F90FLAGS=\"$fopts\" LDFLAGS=\"$lopts\" "
           [[ ! -f a.out ]]  &&  compile_error=true
           continue   # ANDERENFALLS IST STATUS=1, FALLS A.OUT VORHANDEN
        else
-          [[ $localhost = lcxt4 ]]  &&  . /opt/modules/default/init/ksh
+          [[ $localhost = lcxe6 ]]  &&  eval $init_cmds
           [[ "$module_calls" != "" ]]  &&  eval $module_calls
           make $mopts -f Makefile PROG=a.out  F90=$compiler_name  COPT="$cpp_options"  F90FLAGS="$fopts"  LDFLAGS="$lopts"
@@ -3741 +3745 @@
                       mpirun -np $tasks_per_node inspxe-cl -r result -collect mi3 -- ./a.out  <  runfile_atmos
                    fi
-                elif [[ $host = lcxt4  ||  $host = lcxt5m ]]
+                elif [[ $host = lcxe6  ||  $host = lcxt5m ]]
                 then
                     aprun  -n $ii  -N $tasks_per_node  a.out  $ROPTS  < runfile_atmos
@@ -3780 +3784 @@
                       fi
 
-                   elif [[ $host = lcxt4  ||  $host = lcxt5m ]]
+                   elif [[ $host = lcxe6  ||  $host = lcxt5m ]]
                    then
 
@@ -3813 +3817 @@
                       fi
 
-                   elif [[ $host = lcxt4  ||  $host = lcxt5m ]]
+                   elif [[ $host = lcxe6  ||  $host = lcxt5m ]]
                    then
 

palm/trunk/SCRIPTS/subjob

@@ -136 +136 @@
      # 29/11/11 - Siggi - adjustments for lcsgih/lcsgib queues, pingui admitted
      # 21/12/11 - Theres- solano admitted
-     # 31/01/12 - Matthias- adjustments for ibmh
+     # 31/01/12 - Matthias - adjustments for ibmh
+     # 02/05/12 - Bjoern  - lcxt4 is now lcxe6, adjustments for lcxe6, 
+     #                      bugfixes for the parameter file check, initial 
+     #                      commands on ssh calls sourced out to .mrun.config
 
 
@@ -227 +230 @@
      (gregale)               local_addres=130.75.105.109; local_host=lcmuk;;
      (hababai)               local_addres=130.75.105.108; local_host=lcmuk;;
-     (hexagon.bccs.uib.no)   local_addres=129.177.20.113; local_host=lcxt4;;
+     (hexagon.bccs.uib.no)   local_addres=129.177.20.113; local_host=lcxe6;;
      (hd1)                   local_addres=130.75.4.104;   local_host=lcsgih;;
      (hd2)                   local_addres=130.75.4.105;   local_host=lcsgih;;
@@ -242 +245 @@
      (maestro)               local_addres=130.75.105.2;   local_host=lcmuk;;
      (meteo-login*)          local_addres=193.166.211.144;local_host=lcxt5m;;
-     (nid*)                  local_addres=129.177.20.113; local_host=lcxt4;;
+     (hexagon*)              local_addres=129.177.20.113; local_host=lcxe6;;
      (nobel*)                local_addres=150.183.5.101;  local_host=ibms;;
      (orkan)                 local_addres=130.75.105.3;   local_host=lcmuk;;
@@ -390 +393 @@
         (lckordi) remote_addres=210.219.61.8; submcom=/usr/torque/bin/qsub;;
         (lctit)   queue=S; remote_addres=10.1.6.165; submcom=/opt/pbs/tools/bin/t2sub;;
-        (lcxt4)   remote_addres=129.177.20.113; submcom=/opt/torque/2.4.9-snap.201005191035/bin/qsub;;
+        (lcxe6)   remote_addres=129.177.20.113; submcom=/opt/torque/2.5.10/bin/qsub;;
         (lcxt5m)  remote_addres=193.166.211.144; submcom=/opt/pbs/10.1.0.91350/bin/qsub;;
         (lcyon)   remote_addres=165.132.26.68; submcom=/usr/torque/bin/qsub;;
@@ -926 +929 @@
 eval \`/sw/swdist/bin/modulesinit\`
 #. /usr/share/modules/init/bash
+$init_cmds
 $module_calls
 
@@ -945 +949 @@
 eval \`/sw/swdist/bin/modulesinit\`
 #. /usr/share/modules/init/bash
+$init_cmds
 $module_calls
 
@@ -951 +956 @@
     fi
 
- elif [[ $remote_host = lcxt4 ]]
+ elif [[ $remote_host = lcxe6 ]]
  then
 
@@ -969 +974 @@
 $email_directive
 
-. /opt/modules/default/init/ksh
+$init_cmds
 $module_calls
 
@@ -988 +993 @@
 #PBS -o $remote_dayfile
 
-. /opt/modules/default/init/ksh
+$init_cmds
 $module_calls
 
@@ -1036 +1041 @@
 #PBS -o $remote_dayfile
 
-. /opt/modules/default/init/ksh
+$init_cmds
 $module_calls
 
@@ -1053 +1058 @@
 #PBS -o $remote_dayfile
 
-. /opt/modules/default/init/ksh
+$init_cmds
 $module_calls
 
@@ -1141 +1146 @@
     cat > $job_to_send << %%END%%
 #!/bin/ksh
-
+$init_cmds
 $module_calls
 
@@ -1438 +1443 @@
        then
           eval  $submcom  $job_on_remhost
-       elif [[  $local_host = lcfimm  ||  $local_host = lctit  ||  $localhost = lcxt4  ||  $localhost = lck  || $localhost = lckordi||  $localhost = lcyon ]]
+       elif [[  $local_host = lcfimm  ||  $local_host = lctit  ||  $localhost = lcxe6  ||  $localhost = lck  || $localhost = lckordi||  $localhost = lcyon ]]
        then
           chmod  u+x  $job_on_remhost

palm/trunk/SOURCE/check_parameters.f90

@@ -4 +4 @@
 ! Current revisions:
 ! -----------------
-! 
+! Bugfix for parameter file check ( excluding __netcdf4 )
 !
 ! Former revisions:
@@ -2982 +2982 @@
        CONTINUE
 #else
+#if ! defined ( __check )
        message_string = 'NetCDF: NetCDF4 format requested but no ' // &
                         'cpp-directive __netcdf4 given & switch '  // &
@@ -2989 +2990 @@
 #endif
     ENDIF
-
+#endif
 !