Changeset 181 for palm/trunk
- Timestamp:
- Jul 30, 2008 7:07:47 AM (16 years ago)
- Location:
- palm/trunk
- Files:
-
- 10 edited
Legend:
- Unmodified
- Added
- Removed
-
palm/trunk/SCRIPTS/.mrun.config.default
r170 r181 45 45 %fopts -axW:-cpp:-g:-CB:-inline_debug_info:-r8:-nbs:-convert:little:endian lcmuk trace 46 46 %lopts -axW:-cpp:-g:-CB:-inline_debug_info:-r8:-nbs:-Vaxlib lcmuk trace 47 # 48 %sgi_feature ice lcsgih parallel 49 #%remote_username <replace by your HLRN username> lcsgih parallel 50 %compiler_name mpif90 lcsgih parallel 51 %compiler_name_ser ifort lcsgih parallel 52 %cpp_options -DMPI_REAL=MPI_DOUBLE_PRECISION:-DMPI_2REAL=MPI_2DOUBLE_PRECISION:-D__netcdf:-D__netcdf_64bit lcsgih parallel 53 %netcdf_inc -I:/sw/dataformats/netcdf/3.6.2/include lcsgih parallel 54 %netcdf_lib -L/sw/dataformats/netcdf/3.6.2/lib:-lnetcdf:-lnetcdff lcsgih parallel 55 %fopts -g:-w:-xT:-O3:-cpp:-openmp:-r8:-ftz:-fno-alias:-no-prec-div:-no-prec-sqrt:-ip:-nbs:-convert:little_endian lcsgih parallel 56 %lopts -g:-w:-xT:-O3:-cpp:-openmp:-r8:-ftz:-fno-alias:-no-prec-div:-no-prec-sqrt:-ip:-nbs:-Vaxlib:-i-dynamic lcsgih parallel 57 #%tmp_data_catalog /gfs1/work/<replace by your HLRN username>/palm_restart_data lcsgih parallel 58 #%tmp_user_catalog /gfs1/tmp/<replace by your HLRN username> lcsgih parallel 59 # 60 %sgi_feature ice lcsgih parallel debug 61 #%remote_username <replace by your HLRN username> lcsgih parallel debug 62 %compiler_name mpif90 lcsgih parallel debug 63 %compiler_name_ser ifort lcsgih parallel debug 64 %cpp_options -DMPI_REAL=MPI_DOUBLE_PRECISION:-DMPI_2REAL=MPI_2DOUBLE_PRECISION:-D__netcdf:-D__netcdf_64bit lcsgih parallel debug 65 %netcdf_inc -I:/sw/dataformats/netcdf/3.6.2/include lcsgih parallel debug 66 %netcdf_lib -L/sw/dataformats/netcdf/3.6.2/lib:-lnetcdf:-lnetcdff lcsgih parallel debug 67 %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 68 %lopts -C:-fpe0:-debug:-traceback:-g:-w:-xT:-O0:-cpp:-r8:-ftz:-fno-alias:-no-prec-div:-no-prec-sqrt:-ip:-nbs:-Vaxlib:-i-dynamic lcsgih parallel debug 69 #%tmp_data_catalog /gfs1/work/<replace by your HLRN username>/palm_restart_data lcsgih parallel debug 70 #%tmp_user_catalog /gfs1/tmp/<replace by your HLRN username> lcsgih parallel debug 47 71 # 48 72 #%remote_username <replace by your tsubame username> lctit parallel -
palm/trunk/SCRIPTS/mbuild
r169 r181 91 91 # host identifier (local_host) is read from config file 92 92 # 10/10/07 - Siggi - bugfix: handling of comment lines 93 # 18/07/08 - Siggi - adapted for lcsgih 94 # 21/07/08 - Siggi - mainprog (executable) is added to the tar-file 95 # ({mainprog}_current_version) 93 96 94 97 … … 723 726 case $remote_host in 724 727 (lcmuk) remote_addres=130.75.105.2;; 728 (lcsgib) remote_addres=130.73.232.102;; 729 (lcsgih) remote_addres=130.75.4.102;; 725 730 (lctit) remote_addres=172.17.75.161;; 726 731 (decalpha) remote_addres=165.132.26.56;; … … 1299 1304 print "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 1300 1305 1306 elif [[ $remote_host = lcsgib || $remote_host = lcsgih ]] 1307 then 1308 1309 print ". /usr/share/modules/init/bash; module load mvapich/mvapich-0.9.9-intel; 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 1310 # print ". /usr/share/modules/init/bash; module load mvapich2/1.2-intel; 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 1311 1301 1312 elif [[ $remote_host = lctit ]] 1302 1313 then … … 1343 1354 if [[ $remote_host != lctit ]] 1344 1355 then 1345 ssh ${remote_username}@${remote_addres} "cd ${remote_md}; chmod u+w *; tar -cf ${mainprog}_current_version.tar *.f90 *.o *.mod"1356 ssh ${remote_username}@${remote_addres} "cd ${remote_md}; chmod u+w *; tar -cf ${mainprog}_current_version.tar ${mainprog} *.f90 *.o *.mod" 1346 1357 else 1347 1358 # TIT ERLAUBT NUR DIE AUSFÜHRUNG GANZ BESTIMMTER KOMMANDOS 1348 1359 # MIT SSH, DESHALB AUFRUF PER PIPE 1349 print "cd ${remote_md}; chmod u+w *; tar -cf ${mainprog}_current_version.tar *.f90 *.o *.mod" | ssh ${remote_username}@${remote_addres} 2>&11360 print "cd ${remote_md}; chmod u+w *; tar -cf ${mainprog}_current_version.tar ${mainprog} *.f90 *.o *.mod" | ssh ${remote_username}@${remote_addres} 2>&1 1350 1361 fi 1351 1362 -
palm/trunk/SCRIPTS/mrun
r180 r181 581 581 do_remote=true 582 582 case $host in 583 (ibm|ibmb|ibmh|ibms|ibmy|nech|neck|lc tit|unics) true;;583 (ibm|ibmb|ibmh|ibms|ibmy|nech|neck|lcsgib|lcsgih|lctit|unics) true;; 584 584 (*) printf "\n" 585 585 printf "\n +++ sorry: execution of batch jobs on remote host \"$host\"" … … 700 700 do_remote=true 701 701 case $host in 702 (ibm|ibms|ibmy|lc tit|nech|neck|unics) true;;702 (ibm|ibms|ibmy|lcsgib|lcsgih|lctit|nech|neck|unics) true;; 703 703 (*) printf "\n +++ sorry: execution of batch jobs on remote host \"$host\"" 704 704 printf "\n is not available" … … 955 955 do_remote=true 956 956 case $host in 957 (ibm|ibmb|ibmh|ibms|ibmy|lc tit|nech|neck|unics) true;;957 (ibm|ibmb|ibmh|ibms|ibmy|lcsgib|lcsgih|lctit|nech|neck|unics) true;; 958 958 (*) printf "\n" 959 959 printf "\n +++ sorry: execution of batch jobs on remote host \"$host\"" … … 1043 1043 then 1044 1044 node_usage=sla3 1045 elif [[ $(echo $host | cut -c1-5) = lcsgi ]] 1046 then 1047 node_usage=singlejob 1045 1048 else 1046 1049 node_usage=not_shared 1047 1050 fi 1048 1051 fi 1049 if [[ $node_usage != shared && $node_usage != not_shared && "$(echo $node_usage | cut -c1-3)" != "sla" && $node_usage != novice ]] 1052 1053 if [[ $node_usage != shared && $node_usage != not_shared && $node_usage != singlejob && "$(echo $node_usage | cut -c1-3)" != "sla" && $node_usage != novice ]] 1050 1054 then 1051 1055 printf "\n" … … 2244 2248 printf "\n +++ error occured while compiling or linking" 2245 2249 locat=compile 2246 exit 2250 2251 # WORKAROUND: REMOVE IF LATER, BUT KEEP THE EXIT! 2252 if [[ $localhost != lcsgib && $localhost != lcsgih ]] 2253 then 2254 exit 2255 fi 2247 2256 else 2248 2257 printf "$striche\n *** compilation finished \n" … … 2787 2796 if [[ $host = lcsgih || $host = lcsgib ]] 2788 2797 then 2789 echo " --- Content of \$PBS_NODEFILE:" 2790 cat $PBS_NODEFILE 2791 echo " --- end content" 2792 mpirun -machinefile $PBS_NODEFILE -np $ii a.out $ROPTS 2798 # mpirun -machinefile $PBS_NODEFILE -np $ii a.out $ROPTS 2799 ulimit -s 30000 2800 ulimit -a 2801 mpirun_rsh -hostfile $PBS_NODEFILE -np $ii OMP_NUM_THREADS=$OMP_NUM_THREADS palm $ROPTS 2802 # export MV2_NUM_PORTS=2 2803 # export MV2_CPU_MAPPING=0:1:2:3 2804 # mpiexec ./palm $ROPTS 2793 2805 elif [[ $host = lcxt4 ]] 2794 2806 then -
palm/trunk/SCRIPTS/subjob
r179 r181 160 160 (breg*-en0|berni*-en0) local_addres=130.73.230.10; local_host=ibmb;; 161 161 (breva) local_addres=130.75.105.98; local_host=lcmuk;; 162 (b01*) local_addres=130.73.232.102; local_host=lcsgih;; 162 163 (compute-*.local) local_addres=172.20.4.2; local_host=lcfimm;; 163 164 (cs*) local_addres=136.172.44.131; local_host=nech;; … … 172 173 (hexagon.bccs.uib.no) local_addres=129.177.20.113; local_host=lcxt4;; 173 174 (hreg*-en0|hanni*-en0) local_addres=130.75.4.10; local_host=ibmh;; 174 (h01*) local_addres=1 0.152.0.7;local_host=lcsgih;;175 (h01*) local_addres=130.75.4.102; local_host=lcsgih;; 175 176 (irifi) local_addres=130.75.105.104; local_host=lcmuk;; 176 177 (levanto) local_addres=130.75.105.45; local_host=lcmuk;; … … 182 183 (quanero) local_addres=130.75.105.107; local_host=lcmuk;; 183 184 (scirocco) local_addres=172.20.25.41; local_host=lcmuk;; 184 (service100) local_addres=1 0.152.0.7;local_host=lcsgih;;185 (service100) local_addres=130.75.4.102; local_host=lcsgih;; 185 186 (sun1|sun2) local_addres=130.75.6.1; local_host=unics;; 186 (r1*) local_addres=10.152.0.7; local_host=lcsgih;; 187 (r1*) local_addres=130.75.4.102; local_host=lcsgih;; 188 (r2*) local_addres=130.73.232.102; local_host=lcsgih;; 187 189 (tgg*) local_addres=172.17.75.161; local_host=lctit;; 188 190 (vorias) local_addres=172.20.25.43; local_host=lcmuk;; … … 310 312 (ibmy) queue=parallel; remote_addres=165.132.26.58; submcom=/usr/lpp/LoadL/full/bin/llsubmit;; 311 313 (lcfimm) remote_addres=172.20.4.2; submcom=/opt/torque/bin/qsub;; 312 (lcsgih) remote_addres=10.152.0.7; submcom=/opt/moab/bin/msub;; 314 (lcsgib) remote_addres=130.73.232.102; submcom=/opt/torque/bin/qsub;; 315 (lcsgih) remote_addres=130.75.4.102; submcom=/opt/torque/bin/qsub;; 313 316 (lctit) queue=lctit; remote_addres=172.17.75.161; submcom=/n1ge/TITECH_GRID/tools/bin/n1ge;; 314 317 (lcxt4) remote_addres=129.177.20.113; submcom=/opt/torque/2.3.0/bin/qsub;; … … 666 669 fi 667 670 668 elif [[ $remote_host = lcsgih ]]671 elif [[ $remote_host = lcsgih || $remote_host = lcsgib ]] 669 672 then 670 673 … … 672 675 then 673 676 cat > $job_to_send << %%END%% 674 # PBS -S/bin/bash677 #!/bin/bash 675 678 #PBS -N $job_name 676 679 #PBS -l walltime=$timestring 677 #PBS -l nodes=$nodes:ppn=${tasks_per_node}:xe 678 #PBS -l naccesspolicy=singlejob 680 #PBS -l nodes=$nodes:ppn=${tasks_per_node} 681 #PBS -l feature=$sgi_feature 682 #PBS -l naccesspolicy=$node_usage 679 683 #PBS -o $remote_dayfile 680 684 #PBS -j oe … … 682 686 . /usr/share/modules/init/bash 683 687 module load mvapich/mvapich-0.9.9-intel 688 # module load mvapich2/1.2-intel 684 689 module load netcdf 685 export LD_LIBRARY_PATH=/sw/intel/fce/10.1.015/lib:/sw/dataformats/netcdf/3.6.2/lib:$LD_LIBRARY_PATH 686 687 echo ld_library_path=$LD_LIBRARY_PATH 690 export LD_LIBRARY_PATH=/sw/intel/cce/10.1.015/lib:/sw/intel/fce/10.1.015/lib:/sw/dataformats/netcdf/3.6.2/lib:\$LD_LIBRARY_PATH 691 echo ld_library_path=\$LD_LIBRARY_PATH 688 692 689 693 %%END%% … … 860 864 echo "trap '" >> $job_to_send 861 865 echo "set +vx" >> $job_to_send 862 if [[ $(echo $remote_host | cut -c1-3) = ibm || $(echo $remote_host | cut -c1- 3) = nec || $remote_host = lctit ]]866 if [[ $(echo $remote_host | cut -c1-3) = ibm || $(echo $remote_host | cut -c1-5) = lcsgi || $(echo $remote_host | cut -c1-3) = nec || $remote_host = lctit ]] 863 867 then 864 868 if [[ $remote_host = ibmb || $remote_host = ibmh ]] … … 926 930 echo "set -x" >> $job_to_send 927 931 echo "batch_scp -d -w 10 -u $local_user $local_addres $remote_dayfile \"$job_catalog\" $local_dayfile" >> $job_to_send 932 echo "[[ \"\$for_subjob_to_do\" != \"\" ]] && eval \$for_subjob_to_do" >> $job_to_send 933 echo "%%END%%" >> $job_to_send 934 935 elif [[ $(echo $remote_host | cut -c1-5) = lcsgi ]] 936 then 937 echo "cat > scpjob.$kennung << %%END%%" >> $job_to_send 938 echo "#!/bin/bash" >> $job_to_send 939 echo "#PBS -N job_protocol_transfer" >> $job_to_send 940 echo "#PBS -l walltime=00:02:00" >> $job_to_send 941 echo "#PBS -l nodes=1:ppn=1" >> $job_to_send 942 echo "#PBS -l feature=xe" >> $job_to_send 943 echo "#PBS -l naccesspolicy=shared" >> $job_to_send 944 echo "#PBS -o \$HOME/job_queue/last_job_transfer_protocol" >> $job_to_send 945 echo "#PBS -j oe" >> $job_to_send 946 echo " " >> $job_to_send 947 echo ". /usr/share/modules/init/bash" >> $job_to_send 948 echo "set -x" >> $job_to_send 949 echo "batch_scp -d -w 10 -u $local_user $local_addres ${job_catalog}/$remote_dayfile \"$job_catalog\" $local_dayfile" >> $job_to_send 928 950 echo "[[ \"\$for_subjob_to_do\" != \"\" ]] && eval \$for_subjob_to_do" >> $job_to_send 929 951 echo "%%END%%" >> $job_to_send … … 968 990 then 969 991 echo "llsubmit scpjob.$kennung" >> $job_to_send 992 elif [[ $(echo $remote_host | cut -c1-5) = lcsgi ]] 993 then 994 echo "chmod u+x scpjob.$kennung" >> $job_to_send 995 echo "msub scpjob.$kennung" >> $job_to_send 970 996 elif [[ $remote_host = lctit ]] 971 997 then -
palm/trunk/SOURCE/CURRENT_MODIFICATIONS
r179 r181 42 42 Changed: 43 43 ------- 44 Strict grid matching along z is not needed for mg-solver. (check_parameters) 45 44 46 Sharp lateral edges of the plant canopy introduced. Before smaller 45 47 values of the leaf area density than those applied in the prognostic … … 72 74 Workaround for getting information about the coupling mode. (palm) 73 75 74 advec_s_ups, advec_u_ups, advec_v_ups, advec_w_ups, calc_spectra, check_open, init_3d_model, modules, palm, parin, poisfft, read_var_list, read_3d_binary, transpose, write_var_list, write_3d_binary 76 Format adjustments in order to allow CPU# > 999. (cpu_statistics) 77 78 advec_s_ups, advec_u_ups, advec_v_ups, advec_w_ups, calc_spectra, check_open, check_parameters, cpu_statistics, init_3d_model, modules, palm, parin, poisfft, read_var_list, read_3d_binary, transpose, write_var_list, write_3d_binary 75 79 76 80 77 81 Errors: 78 82 ------ 83 Bugfix: zero assignments to tendency arrays in case of restarts (init_3d_model) 84 85 Bugfix: wrong grid level used in multigrid solver, routine restrict (poismg) 86 79 87 Bugfix: Construction of vertical profiles when 10 gradients have been 80 88 specified in the parameter list (ug, vg, pt, q, sa, lad). (check_parameters) … … 109 117 110 118 111 check_parameters, flow_statistics, init_dvrp, local_stop, plant_canopy_model, pres, read_3d_binary, user_interface, write_3d_binary119 check_parameters, flow_statistics, init_dvrp, init_3d_model, local_stop, plant_canopy_model, poismg, pres, read_3d_binary, user_interface, write_3d_binary 112 120 -
palm/trunk/SOURCE/check_parameters.f90
r177 r181 5 5 ! ----------------- 6 6 ! Bug fix: Construction of vertical profiles when 10 gradients have been 7 ! specified in the parameter list (ug, vg, pt, q, sa, lad) 8 ! 7 ! specified in the parameter list (ug, vg, pt, q, sa, lad) 8 ! 9 ! Strict grid matching along z is not needed for mg-solver. 9 10 ! Leaf area density (LAD) explicitly set to its surface value at k=0 10 11 ! Case of reading data for recycling included in initializing_actions, … … 369 370 CALL local_stop 370 371 ENDIF 371 IF ( ( psolver == 'poisfft_hybrid' .OR. psolver == 'multigrid' ) .AND. & 372 ( nxra > nxr .OR. nyna > nyn .OR. nza > nz ) ) THEN 372 IF ( psolver == 'poisfft_hybrid' .AND. & 373 ( nxra > nxr .OR. nyna > nyn .OR. nza > nz ) .OR. & 374 psolver == 'multigrid' .AND. & 375 ( nxra > nxr .OR. nyna > nyn ) ) THEN 373 376 IF ( myid == 0 ) THEN 374 377 PRINT*, '+++ check_parameters:' -
palm/trunk/SOURCE/cpu_statistics.f90
r83 r181 4 4 ! Actual revisions: 5 5 ! ----------------- 6 ! 6 ! Format adjustments in order to allow CPU# > 999 7 7 ! 8 8 ! Former revisions: … … 125 125 CALL check_open( 18 ) 126 126 WRITE ( 18, 100 ) TRIM( run_description_header ), & 127 numprocs * threads_per_task, numprocs, &127 numprocs * threads_per_task, pdims(1), pdims(2), & 128 128 threads_per_task 129 129 DO … … 249 249 250 250 251 100 FORMAT (A/11('-')//'CPU measures for ',I3,' PEs (',I3,' tasks *',I3, & 252 &' threads):'/ & 253 &'--------------------------------------------------'// & 251 100 FORMAT (A/11('-')//'CPU measures for ',I5,' PEs (',I5,'(x) * ',I5,'(y', & 252 &') tasks *',I5,' threads):'/ & 253 &'----------------------------------------------------------', & 254 &'------------'//& 254 255 &'place: mean counts min ', & 255 256 &' max rms'/ & -
palm/trunk/SOURCE/init_3d_model.f90
r163 r181 7 7 ! Actual revisions: 8 8 ! ----------------- 9 ! Bugfix: zero assignments to tendency arrays in case of restarts 9 10 ! Further amendments to and modifications in the initialisation of the plant 10 11 ! canopy model 11 12 ! Allocation of hom_sum moved to parin, initialization of spectrum_x|y directly 12 13 ! after allocating theses arrays, 13 ! read data for recycling added as new initialization option 14 ! read data for recycling added as new initialization option, 15 ! dummy allocation for diss 14 16 ! 15 17 ! Former revisions: … … 235 237 IF ( use_sgs_for_particles ) THEN 236 238 ALLOCATE ( diss(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1) ) 239 ELSE 240 ALLOCATE ( diss(2,2,2) ) ! required because diss is used as a 241 ! formal parameter 237 242 ENDIF 238 243 … … 1046 1051 IF ( humidity .OR. passive_scalar ) q_p = q 1047 1052 IF ( ocean ) sa_p = sa 1053 1054 ! 1055 !-- Allthough tendency arrays are set in prognostic_equations, they have 1056 !-- have to be predefined here because they are used (but multiplied with 0) 1057 !-- there before they are set. 1058 IF ( timestep_scheme(1:5) == 'runge' ) THEN 1059 te_m = 0.0; tpt_m = 0.0; tu_m = 0.0; tv_m = 0.0; tw_m = 0.0 1060 IF ( humidity .OR. passive_scalar ) tq_m = 0.0 1061 IF ( ocean ) tsa_m = 0.0 1062 ENDIF 1048 1063 1049 1064 ELSE -
palm/trunk/SOURCE/init_pegrid.f90
r163 r181 4 4 ! Actual revisions: 5 5 ! ----------------- 6 ! ATTENTION: nnz_x undefined problem still has to be solved!!!!!!!! 7 ! nz is used instead nnz for calculating mg-levels 6 8 ! Collect on PE0 horizontal index bounds from all other PEs, 7 9 ! broadcast the id of the inflow PE (using the respective communicator) … … 340 342 341 343 sendrecvcount_zx = nnx * nny * nnz_x 344 345 ELSE 346 ! 347 !--- Setting of dummy values because otherwise variables are undefined in 348 !--- the next step x --> y 349 !--- WARNING: This case has still to be clarified!!!!!!!!!!!! 350 nnz_x = 1 351 nzb_x = 1 352 nzt_xa = 1 353 nzt_x = 1 354 nny_x = nny 342 355 343 356 ENDIF … … 694 707 ENDDO 695 708 696 k = nnz 709 k = nz ! do not use nnz because it might be > nz due to transposition 710 ! requirements 697 711 DO WHILE ( MOD( k, 2 ) == 0 .AND. k /= 2 ) 698 712 k = k / 2 -
palm/trunk/SOURCE/poismg.f90
r139 r181 8 8 ! Actual revisions: 9 9 ! ----------------- 10 ! 10 ! Bugfix: grid_level+1 has to be used in restrict for flags-array 11 11 ! 12 12 ! Former revisions: … … 274 274 ! 275 275 !-- Choose flag array of the upper level 276 SELECT CASE ( l )276 SELECT CASE ( l+1 ) 277 277 CASE ( 1 ) 278 278 flags => wall_flags_1
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