[Wien] PBS run
Dear All, I am trying to run WIEN2k parallel. My shell script is looking like this. However, in the out.log file it is showing -- lapw0: Command not found. > stop error --- please help. ### script ## #!/bin/bash #PBS -N wien2k #PBS -o out.log #PBS -j oe #PBS -l nodes=1:ppn=1 # Load Intel environment source /apps/intel_2016_u2/compilers_and_libraries_2016.2.181/linux/bin/compilervars.sh intel64 cd /home/sjana/WIEN2k/PBE/C_pbe rm -f .machines echo '#' > .machines echo 'granularity:1' >>.machines awk '{print "1:"$1":1"}' $PBS_NODEFILE >>.machines echo 'extrafine:1' >>.machines /home/sjana/WIEN2k_14.2/run_lapw -p -i 40 -ec .0001 -I Regards, S. Jana ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
[Wien] PBS run
Hi Gavin Abo, I change my job script as follows: # #!/bin/bash #PBS -N wien2k #PBS -o out.log #PBS -j oe #PBS -l nodes=1:ppn=1 # Load Intel environment source /apps/intel_2016_u2/compilers_and_libraries_2016.2.181/linux/bin/compilervars.sh intel64 cd /home/sjana/WIEN2k/PBE/C_pbe rm -f .machines echo '#' > .machines *echo -n 'lapw0:' > .machines* echo 'granularity:1' >>.machines awk '{print "1:"$1":1"}' $PBS_NODEFILE >>.machines echo 'extrafine:1' >>.machines /home/sjana/WIEN2k_14.2/run_lapw -p -i 40 -ec .0001 -I ### Now the out.log awk: cmd. line:1: fatal: cannot open file `-np' for reading (No such file or directory) ssh: Could not resolve hostname granularity: Name or service not known^M > stop error Regards, S. Jana ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
[Wien] PBS run
Hi Gavin Abo, It looks I am facing the same problem. ## #!/bin/bash #PBS -N wien2k #PBS -o out.log #PBS -j oe #PBS -l nodes=1:ppn=1 # Load Intel environment source /apps/intel_2016_u2/compilers_and_libraries_2016.2.181/linux/bin/compilervars.sh intel64 export OMP_NUM_THREADS=1 cd /home/sjana/WIEN2k/PBE/C_pbe rm -f .machines #source /apps/intel_2016_u2/compilers_and_libraries_2016.2.181/linux/bin/compilervars.sh intel64 cd /home/sjana/WIEN2k/PBE/C_pbe rm -f .machines echo '#' > .machines echo -n 'lapw0:' > .machines echo 'granularity:1' >>.machines #awk '{print "1:"$1":1"}' $PBS_NODEFILE >>.machines awk '{print "1:"$1":1"}' "$PBS_NODEFILE" >>.machines echo 'extrafine:1' >>.machines #/home/sjana/WIEN2k_14.2/run_lapw -p -i 40 -ec .0001 -I run_lapw -p -i 40 -ec .0001 -I # My .machines file looks like lapw0:granularity:1 1:r8n3:1 extrafine:1 out.log ssh: Could not resolve hostname granularity: Name or service not known^M > stop error Regards, S. Jana ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] PBS run
Does lapw0 exist in your WIEN2k directory (/home/sjana/WIEN2k_14.2)? Maybe #PBS -V is needed [ https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg15985.html ]. On 9/8/2017 1:42 AM, Subrata Jana wrote: Dear All, I am trying to run WIEN2k parallel. My shell script is looking like this. However, in the out.log file it is showing -- lapw0: Command not found. > stop error --- please help. ### script ## #!/bin/bash #PBS -N wien2k #PBS -o out.log #PBS -j oe #PBS -l nodes=1:ppn=1 # Load Intel environment source /apps/intel_2016_u2/compilers_and_libraries_2016.2.181/linux/bin/compilervars.sh intel64 cd /home/sjana/WIEN2k/PBE/C_pbe rm -f .machines echo '#' > .machines echo 'granularity:1' >>.machines awk '{print "1:"$1":1"}' $PBS_NODEFILE >>.machines echo 'extrafine:1' >>.machines /home/sjana/WIEN2k_14.2/run_lapw -p -i 40 -ec .0001 -I Regards, S. Jana ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] PBS run
It look like something is wrong with this line [ https://stackoverflow.com/questions/26816605/awk-fatal-cannot-open-file-for-reading-no-such-file-or-directory ]: awk '{print "1:"$1":1"}' $PBS_NODEFILE >>.machines Maybe quotes are needed around the $PBS_NODEFILE: awk '{print "1:"$1":1"}' "$PBS_NODEFILE" >>.machines On 9/8/2017 2:20 AM, Subrata Jana wrote: Hi Gavin Abo, I change my job script as follows: # #!/bin/bash #PBS -N wien2k #PBS -o out.log #PBS -j oe #PBS -l nodes=1:ppn=1 # Load Intel environment source /apps/intel_2016_u2/compilers_and_libraries_2016.2.181/linux/bin/compilervars.sh intel64 cd /home/sjana/WIEN2k/PBE/C_pbe rm -f .machines echo '#' > .machines *echo -n 'lapw0:' > .machines* echo 'granularity:1' >>.machines awk '{print "1:"$1":1"}' $PBS_NODEFILE >>.machines echo 'extrafine:1' >>.machines /home/sjana/WIEN2k_14.2/run_lapw -p -i 40 -ec .0001 -I ### Now the out.log awk: cmd. line:1: fatal: cannot open file `-np' for reading (No such file or directory) ssh: Could not resolve hostname granularity: Name or service not known^M > stop error Regards, S. Jana ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] PBS run
You might have a look at the "WIEN2k-notes of the University of Texas" document (slide 7) at: http://susi.theochem.tuwien.ac.at/reg_user/faq/pbs.html The line: echo -n 'lapw0:' > .machines It looks like that writes to the .machines file: lapw0: However, you need to have it write the "machine names" after it. So something like: lapw0:gamma:2 delta:2 epsilon:4 However, you are having it write: lapw0:granularity:1 Thus, the error about it not being able to find and connect to a hostname called "granularity". On 9/8/2017 2:41 AM, Subrata Jana wrote: Hi Gavin Abo, It looks I am facing the same problem. ## #!/bin/bash #PBS -N wien2k #PBS -o out.log #PBS -j oe #PBS -l nodes=1:ppn=1 # Load Intel environment source /apps/intel_2016_u2/compilers_and_libraries_2016.2.181/linux/bin/compilervars.sh intel64 export OMP_NUM_THREADS=1 cd /home/sjana/WIEN2k/PBE/C_pbe rm -f .machines #source /apps/intel_2016_u2/compilers_and_libraries_2016.2.181/linux/bin/compilervars.sh intel64 cd /home/sjana/WIEN2k/PBE/C_pbe rm -f .machines echo '#' > .machines echo -n 'lapw0:' > .machines echo 'granularity:1' >>.machines #awk '{print "1:"$1":1"}' $PBS_NODEFILE >>.machines awk '{print "1:"$1":1"}' "$PBS_NODEFILE" >>.machines echo 'extrafine:1' >>.machines #/home/sjana/WIEN2k_14.2/run_lapw -p -i 40 -ec .0001 -I run_lapw -p -i 40 -ec .0001 -I # My .machines file looks like lapw0:granularity:1 1:r8n3:1 extrafine:1 out.log ssh: Could not resolve hostname granularity: Name or service not known^M > stop error Regards, S. Jana ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html