[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
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[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
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[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
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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
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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
___
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http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
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Wien@zeus.theochem.tuwien.ac.at
http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
SEARCH the MAILING-LIST at:
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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
___
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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
