Changeset 2257 for palm/trunk/SCRIPTS
- Timestamp:
- Jun 7, 2017 2:07:05 PM (7 years ago)
- Location:
- palm/trunk/SCRIPTS
- Files:
-
- 3 edited
Legend:
- Unmodified
- Added
- Removed
-
palm/trunk/SCRIPTS/mbuild
r1945 r2257 27 27 # ----------------- 28 28 # $Id$ 29 # adjustments for lceddy, removed lcflow-specific code 30 # 31 # 1945 2016-06-15 07:17:24Z raasch 29 32 # 30 33 # 1944 2016-06-15 06:29:00Z raasch … … 528 531 (lccrayb) remote_address=130.73.233.1;; 529 532 (lccrayh) remote_address=130.75.4.1;; 530 (lcflow) remote_address="flow02.hpc.uni-oldenburg.de";;531 533 (lckordi) remote_adress=210.219.61.8;; 532 534 (lcmuk) remote_address=130.75.105.2;; … … 1371 1373 then 1372 1374 . $modules 1373 elif [[ $remote_host = lcflow]]1374 then 1375 eval `$MODULESHOME/ bin/modulecmd ksh load ${modules}`1375 elif [[ $remote_host = lceddy ]] 1376 then 1377 eval `$MODULESHOME/libexec/lmod load ${modules}` 1376 1378 else 1377 1379 eval init_cmds=$init_cmds -
palm/trunk/SCRIPTS/mrun
r2186 r2257 27 27 # ----------------- 28 28 # $Id$ 29 # adjustments for lceddy, removed lcflow-specific code 30 # 31 # 2186 2017-03-21 05:36:31Z raasch 29 32 # 30 33 # 2185 2017-03-21 05:09:29Z raasch … … 652 655 do_remote=true 653 656 case $host in 654 (ibm|ibmh|ibmkisti|ibmku|ibms|nech|lcbullhh|lccrayb|lccrayh|lccrayf|lc flow|lckyoto|lcocean|unics|lcxe6|lcxt5m|lck|lckiaps|lckordi|lckyuh|lckyut|lcsb) true;;657 (ibm|ibmh|ibmkisti|ibmku|ibms|nech|lcbullhh|lccrayb|lccrayh|lccrayf|lceddy|lckyoto|lcocean|unics|lcxe6|lcxt5m|lck|lckiaps|lckordi|lckyuh|lckyut|lcsb) true;; 655 658 (*) printf "\n" 656 659 printf "\n +++ sorry: execution of batch jobs on remote host \"$host\"" … … 810 813 do_remote=true 811 814 case $host in 812 (ibm|ibmh|ibmkisti|ibmku|ibms|lcbullhh|lccrayb|lccrayh|lccrayf|lc flow|lckyoto|lcocean|nech|unics|lcxe6|lcxt5m|lck|lckiaps|lckordi|lckyuh|lckyut|lcsb) true;;815 (ibm|ibmh|ibmkisti|ibmku|ibms|lcbullhh|lccrayb|lccrayh|lccrayf|lceddy|lckyoto|lcocean|nech|unics|lcxe6|lcxt5m|lck|lckiaps|lckordi|lckyuh|lckyut|lcsb) true;; 813 816 (*) printf "\n +++ sorry: execution of batch jobs on remote host \"$host\"" 814 817 printf "\n is not available" … … 1074 1077 do_remote=true 1075 1078 case $host in 1076 (ibm|ibmh|ibmkisti|ibmku|ibms|lcbullhh|lccrayb|lccrayh|lccrayf|lc flow|lckyoto|lcocean|nech|unics|lcxe6|lcxt5m|lck|lckiaps|lckordi|lckyuh|lckyut|lcsb) true;;1079 (ibm|ibmh|ibmkisti|ibmku|ibms|lcbullhh|lccrayb|lccrayh|lccrayf|lceddy|lckyoto|lcocean|nech|unics|lcxe6|lcxt5m|lck|lckiaps|lckordi|lckyuh|lckyut|lcsb) true;; 1077 1080 (*) printf "\n" 1078 1081 printf "\n +++ sorry: execution of batch jobs on remote host \"$host\"" … … 1103 1106 # CHECK, IF THE NUMBER OF CORES PER NODE HAS BEEN GIVEN UND IF IT IS AN 1104 1107 # INTEGRAL DIVISOR OF THE TOTAL NUMBER OF CORES GIVEN BY OPTION -X 1105 if [[ "$tasks_per_node" = "" && $host != lc flow && $host != lcxt5m ]]1108 if [[ "$tasks_per_node" = "" && $host != lcxt5m ]] 1106 1109 then 1107 1110 printf "\n" … … 1119 1122 fi 1120 1123 1121 if [[ $host != lc flow && $host != lcxt5m ]]1124 if [[ $host != lcxt5m ]] 1122 1125 then 1123 1126 (( nodes = numprocs / ( tasks_per_node * threads_per_task ) )) … … 2421 2424 [[ ! -f a.out ]] && compile_error=true 2422 2425 continue # STATUS=1, IF a.out EXISTS 2423 elif [[ $localhost = lcflow ]]2424 then2425 printf " compiler is called via ssh on \"flow\" \n"2426 /usr/bin/ssh $SSH_PORTOPT 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\" "2427 check_for_file=`/usr/bin/ssh $SSH_PORTOPT flow02.hpc.uni-oldenburg.de -l $usern "ls $TEMPDIR/a.out 2> /dev/null"`2428 [[ "$check_for_file" = "" ]] && compile_error=true2429 continue # STATUS=1, IF a.out EXISTS2430 2426 elif [[ $localhost = lcbullhh || $localhost = lccrayb || $localhost = lccrayf || $localhost = lccrayh ]] 2431 2427 then 2428 make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts" 2429 elif [[ $localhost = lceddy ]] 2430 then 2431 which mpifc 2432 2432 make $mopts -f Makefile PROG=a.out F90=$compiler_name COPT="$cpp_options" F90FLAGS="$fopts" LDFLAGS="$lopts" 2433 2433 else … … 3100 3100 # COPY HOSTFILE FROM SOURCE DIRECTORY OR CREATE IT, IF IT 3101 3101 # DOES NOT EXIST 3102 if [[ $host != lcbullhh && $host != lccrayb && $host != lccrayf && $host != lccrayh && $host != lckyuh && $host != lckyut && $host != lcocean ]]3102 if [[ $host != lcbullhh && $host != lccrayb && $host != lccrayf && $host != lccrayh && $host != lckyuh && $host != lckyut && $host != lcocean && $host != lceddy ]] 3103 3103 then 3104 3104 if [[ -f $hostfile ]] … … 3167 3167 elif [[ $host = lcxe6 || $host = lcxt5m ]] 3168 3168 then 3169 aprun -n $ii -N $tasks_per_node a.out < runfile_atmos 3170 elif [[ $host = lcflow ]] 3171 then 3172 mpirun -np $ii a.out < runfile_atmos 3169 aprun -n $ii -N $tasks_per_node a.out < runfile_atmos 3170 elif [[ $host = lceddy ]] 3171 then 3172 echo $ii 3173 echo $tasks_per_node 3174 echo $nodes 3175 mpirun -n $ii a.out < runfile_atmos 3173 3176 elif [[ $host = lcocean ]] 3174 3177 then … … 3177 3180 then 3178 3181 mpirun_rsh -hostfile $PBS_NODEFILE -np `cat $PBS_NODEFILE | wc -l` a.out < runfile_atmos 3182 3179 3183 elif [[ $host = lckiaps ]] 3180 3184 then … … 4081 4085 then 4082 4086 4083 if [[ $localhost = lcbullhh || $localhost = lccrayb || $localhost = lccrayh || $localhost = nech || $localhost = ibmh || $localhost = ibmkisti || $localhost = ibmku || $localhost = ibms || $localhost = lc flow|| $localhost = lckyu* || $localhost = lcxe6 ]]4087 if [[ $localhost = lcbullhh || $localhost = lccrayb || $localhost = lccrayh || $localhost = nech || $localhost = ibmh || $localhost = ibmkisti || $localhost = ibmku || $localhost = ibms || $localhost = lceddy || $localhost = lckyu* || $localhost = lcxe6 ]] 4084 4088 then 4085 4089 echo "*** ssh will be used to initiate restart-runs!" … … 4110 4114 then 4111 4115 ssh $SSH_PORTOPT $usern@gaiad "ssh $SSH_PORTOPT $return_address -l $return_username \"PATH=\\\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc\" " 4112 elif [[ $localhost = lc flow]]4116 elif [[ $localhost = lceddy ]] 4113 4117 then 4114 4118 /usr/bin/ssh $SSH_PORTOPT $return_address -l $return_username "PATH=\$PATH:$LOCAL_MRUN_PATH;export PALM_BIN=$LOCAL_MRUN_PATH;cd $LOCAL_PWD; $mc " … … 4496 4500 echo "export LOCAL_MRUN_PATH" >> $jobfile 4497 4501 4498 # lc flowALSO REQUIRES TO PROVIDE PATH FOR THE PALM-SCRIPTS4499 # if [[ $host = lcflow || $localhost = lcflow]]4500 #then4502 # lceddy ALSO REQUIRES TO PROVIDE PATH FOR THE PALM-SCRIPTS 4503 if [[ $host = lceddy || $localhost = lceddy ]] 4504 then 4501 4505 echo "export PALM_BIN=$PALM_BIN" | sed -e 's:'$HOME':$HOME:' >> $jobfile 4502 4506 echo "export PATH=\$PATH:\$PALM_BIN" >> $jobfile 4503 #fi4507 fi 4504 4508 4505 4509 # CALL MRUN WITHIN THE JOB (SETTING QUEUE IS A WORKAROUND FOR ibmkisti) -
palm/trunk/SCRIPTS/subjob
r2188 r2257 28 28 # ----------------- 29 29 # $Id$ 30 # adjustments for lceddy, removed lcflow-specific code 31 # 32 # 2188 2017-03-21 06:42:42Z raasch 30 33 # 31 34 # 2187 2017-03-21 06:41:25Z raasch … … 230 233 (cs*) local_address=136.172.44.131; local_host=nech;; 231 234 (elephanta) local_address=130.75.105.6; local_host=lcmuk;; 232 ( flow01) local_address=10.141.255.71; local_host=lcflow;;233 ( flow02) local_address=10.141.255.72; local_host=lcflow;;235 (hpcl*) local_address=eddy.hpc.uni-oldenburg.de; local_host=lceddy;; 236 (cfd*) local_address=eddy.hpc.uni-oldenburg.de; local_host=lceddy;; 234 237 (node*) local_address=165.132.26.61 local_host=lck;; 235 238 # (node*) local_address=210.219.61.8 local_host=lckordi;; … … 404 407 (lccrayh) queue=mpp1testq; remote_address=130.75.4.1; submcom="/opt/moab/default/bin/msub -E";; 405 408 (lccrayf) queue=small; remote_address=86.50.166.21; submcom=/opt/slurm/default/bin/sbatch;; 406 (lc flow) remote_address=10.140.1.72; submcom=qsub;;409 (lceddy) remote_address=eddy.hpc.uni-oldenburg.de; submcom=sbatch;; 407 410 (lckyoto) remote_address=133.3.51.11; submcom=/thin/local/bin/qsub;; 408 411 (lck) remote_address=165.132.26.61; submcom=/usr/torque/bin/qsub;; … … 466 469 (*) error=true;; 467 470 esac;; 468 (lc flow) case $ndq in469 ( cfd_lom_long.q|cfd_him_long.q|cfd_lom_serl.q|cfd_lom_shrt.q|cfd_him_shrt.q|cfd_ivy_shrt.q) error=false;;471 (lceddy) case $ndq in 472 (eddy.p|cfdh.p|cfdl.p|carl.p|mpcs.p|mpcl.p|mpcb.p|all_nodes.p) error=false;; 470 473 (*) error=true;; 471 474 esac;; … … 924 927 fi 925 928 926 elif [[ $remote_host = lcflow ]] 927 then 928 if [[ $numprocs != 0 ]] 929 then 930 pe_set="#$ -pe impi $numprocs" 931 else 932 pe_set="#$ -pe impi 1" 933 fi 934 if [[ $queue = default ]] 935 then 936 queue_set="" 937 else 938 queue_set="#$ -q $queue" 939 fi 940 [[ "$disc_space" = "" ]] && disc_space=50 941 942 cat > $job_to_send << %%END%% 929 930 931 elif [[ $remote_host = lceddy ]] 932 then 933 cat > $job_to_send << %%END%% 943 934 #!/bin/bash 944 #$ -S /bin/bash 945 #$ -N $job_name 946 #$ -cwd 947 #$ -l h_rt=$timestring 948 #$ -l h_vmem=${memory}M 949 #$ -o $remote_dayfile 950 #$ -j y 951 $pe_set 952 #$ -R y 953 #$ -l h_fsize=${disc_space}G 954 $queue_set 935 #SBATCH -J $job_name 936 #SBATCH -t $timestring 937 #SBATCH -n $numprocs 938 #SBATCH -N $nodes 939 #SBATCH --cpus-per-task 1 940 #SBATCH -p $queue 941 #SBATCH -o $remote_dayfile 942 #SBATCH -e $remote_dayfile 943 #SBATCH --mem-per-cpu $memory 944 #SBATCH --exclusive 945 946 module load PALMDependencies/.gcc 947 948 $init_cmds 949 $module_calls 955 950 956 951 %%END%% … … 1288 1283 echo "trap '" >> $job_to_send 1289 1284 echo "set +vx" >> $job_to_send 1290 if [[ $(echo $remote_host | cut -c1-3) = ibm || $remote_host = lcbullhh || $remote_host = lccrayb || $remote_host = lccrayh || $(echo $remote_host | cut -c1-3) = nec || $remote_host = lc flow || $remote_host = lckiaps || $remote_host = lckyu* || $remote_host = lcxe6 || $remote_host = lcocean ]]1285 if [[ $(echo $remote_host | cut -c1-3) = ibm || $remote_host = lcbullhh || $remote_host = lccrayb || $remote_host = lccrayh || $(echo $remote_host | cut -c1-3) = nec || $remote_host = lckiaps || $remote_host = lckyu* || $remote_host = lcxe6 || $remote_host = lcocean ]] 1291 1286 then 1292 1287 if [[ $remote_host = ibmh ]] … … 1461 1456 echo "rm -f scpjob.${identifier}.tmp" >> $job_to_send 1462 1457 1463 elif [[ $remote_host = lcflow ]]1464 then1465 echo "cat > scpjob.${identifier}.tmp << %%END%%" >> $job_to_send1466 echo "#!/bin/bash" >> $job_to_send1467 echo "SGEPREFIX -S /bin/bash" >> $job_to_send1468 echo "SGEPREFIX -N transfer_$job_name" >> $job_to_send1469 echo "SGEPREFIX -cwd" >> $job_to_send1470 echo "SGEPREFIX -l h_rt=01:00:00" >> $job_to_send1471 echo "SGEPREFIX -l h_vmem=500M" >> $job_to_send1472 echo "SGEPREFIX -j y" >> $job_to_send1473 echo "SGEPREFIX -o ${local_host}_${job_name}_scpjob_$identifier" >> $job_to_send1474 echo " " >> $job_to_send1475 echo "set -x" >> $job_to_send1476 echo "export PALM_BIN=$PALM_BIN" | sed -e 's:'$HOME':$HOME:' >> $job_to_send1477 echo "export PATH=\$PATH:\$PALM_BIN" >> $job_to_send1478 echo "" >> $job_to_send1479 echo "batch_scp $PORTOPT -d -w 10 -u $local_user $local_address ${job_catalog}/$remote_dayfile \"$job_catalog\" $local_dayfile" >> $job_to_send1480 echo "[[ \"\$for_subjob_to_do\" != \"\" ]] && eval \$for_subjob_to_do" >> $job_to_send1481 echo "rm -f scpjob.${identifier}" >> $job_to_send1482 echo "%%END%%" >> $job_to_send1483 echo "sed -e 's/SGEPREFIX/#$/g' scpjob.${identifier}.tmp > scpjob.${identifier}" >> $job_to_send1484 echo "rm -f scpjob.${identifier}.tmp" >> $job_to_send1485 1458 elif [[ $remote_host = lcxe6 ]] 1486 1459 then … … 1549 1522 echo "scp $PORTOPT scpjob.$identifier ${remote_username}@${remote_address}:job_queue" >> $job_to_send 1550 1523 echo "ssh $SSH_PORTOPT ${remote_username}@${remote_address} \"cd job_queue; $submcom scpjob.$identifier; rm scpjob.$identifier\" " >> $job_to_send 1551 elif [[ $remote_host = lc flow || $remote_host = lcocean ]]1524 elif [[ $remote_host = lcocean ]] 1552 1525 then 1553 1526 echo "mv scpjob.$identifier $job_catalog" >> $job_to_send … … 1585 1558 1586 1559 # REMOVE JOB-FILE 1587 if [[ $remote_host = lctit || $remote_host = ibmku || $remote_host = lcflow]]1560 if [[ $remote_host = lctit || $remote_host = ibmku ]] 1588 1561 then 1589 1562 echo " " >> $job_to_send … … 1638 1611 then 1639 1612 ssh $SSH_PORTOPT $remote_address -l $remote_user "cd $job_catalog; $submcom $job_on_remhost" 1640 elif [[ $remote_host = lcflow ]]1641 then1642 /usr/bin/ssh $SSH_PORTOPT $remote_address -l $remote_user "$init_cmds $module_calls cd $job_catalog; $submcom $job_on_remhost"1643 1613 else 1644 1614 ssh $ssh_key $SSH_PORTOPT $remote_address -l $remote_user "cd $job_catalog; $submcom $job_on_remhost; rm $job_on_remhost" … … 1648 1618 else 1649 1619 cd $job_catalog 1650 if [[ $(echo $local_host | cut -c1-3) = ibm || $(echo $local_host | cut -c1-6) = lccray ]]1620 if [[ $(echo $local_host | cut -c1-3) = ibm || $(echo $local_host | cut -c1-6) = lccray || $local_host = lceddy ]] 1651 1621 then 1652 1622 eval $submcom $job_on_remhost … … 1673 1643 fi 1674 1644 1675 # JOBFILE MUST NOT BE DELETED ON lctit/ibmku /lcflow. THIS WILL BE DONE1645 # JOBFILE MUST NOT BE DELETED ON lctit/ibmku. THIS WILL BE DONE 1676 1646 # AT THE END OF THE JOB 1677 if [[ $local_host != lctit && $local_host != ibmku && $local_host != lcflow]]1647 if [[ $local_host != lctit && $local_host != ibmku ]] 1678 1648 then 1679 1649 rm $job_on_remhost
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