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3. Save, process, and post-process (see [2]−2)\\
3. Save, process, and post-process if necessary (see [2]−2)\\
3. Save, process, and post-process (see [2]−2)
3. Save, process, and post-process if necessary (see [2]−2)
2. If processing still doesn’t go well or you don’t want to comment out the lines causing a problem to processing, you may have to turn off all post processing scripts. To do this, go to UMUI: [local post-processing scripts] and set “N
” to all lines there. (You could find out which one is disturbing the processing by turning on and off from one script to another and try processing.) So now post processing needs to be done manually every time after processing.
2. If processing still doesn’t go well or you don’t want to comment out the lines causing a problem in processing, you may have to turn off all post processing scripts. To do this, go to UMUI: [local post-processing scripts] and set “N
” to all lines there. (You could find out which one is disturbing the processing by turning on and off from one script to another and try processing.) So now post processing needs to be done manually every time after processing.
2. If processing still doesn’t go well you may have to turn off all post processing scripts. To do this, go to UMUI: [local post-processing scripts] and set “N
” to all lines there. (You could find out which one is disturbing the processing by turning on and off from one script to another and try processing.) So now post processing needs to be done manually every time after processing.
2. If processing still doesn’t go well or you don’t want to comment out the lines causing a problem to processing, you may have to turn off all post processing scripts. To do this, go to UMUI: [local post-processing scripts] and set “N
” to all lines there. (You could find out which one is disturbing the processing by turning on and off from one script to another and try processing.) So now post processing needs to be done manually every time after processing.
1. in my first attempts UMUI froze during processing. it was found that the following lines in my puma:~/.kshrc
were somehow disturbing the processing;
1. in my first attempts UMUI froze during processing. it was found (by Annette, Thanks!) that the following lines in my puma:~/.kshrc
were somehow disturbing the processing;
so I commented out these lines.\\
also
--- Make ^H into erase if /usr/bin/tty -s ;then stty erase ^H fi
so I commented out these lines.
2. If processing still doesn’t go well you may have to turn off all post processing scripts. To do this, go to UMUI: [local post-processing scripts] and set “N
” to all lines there. (You could find out which one is disturbing the processing by turning on and off from one script to another and try processing.) So now post processing needs to be done manually every time after processing.
/home/famous/bin/he_namelist_new_phase5 [jobid]
/home/famous/bin/vfdrift_pp.sh [jobid]
/home/famous/bin/quest_queue.sh [jobid]
2. processing still didn’t go well and that was because of the post processing. I could avoid this problem by setting all post processing scripts to “N
” in [local post-processing scripts] in UMUI. (You could find out which one is disturbing the processing by turning on and off from one script to another and try processing, but it was found that I have to turn off all scripts in my case.) So now post processing needs to be done manually every time after processing.
/home/famous/bin/he_namelist_new_phase5 [jobid]
/home/famous/bin/vfdrift_pp.sh [jobid]
/home/famous/bin/quest_queue.sh [jobid]
The compilation and the run must be done in separate stages.\\
The compilation and the run must be done in separate stages.
\\
For basic procedures to run FAMOUS version 4.5.3 on the QUEST cluster, look at RunningQuest. Here I put some notes from my own experience of running a copy of xcpsb [tcmia] (although these contain some repetition of the Running Quest page to provide the contexts). Similar notes for running with reconfiguration are also available here.\\
For basic procedures to run FAMOUS version 4.5.3 on the QUEST cluster, look at RunningQuest. Here I put some notes from my own experience of running a copy of xcpsb [tcmia] (although these contain some repetition of the Running Quest page to provide the contexts). Similar notes for running FAMOUS with reconfiguration are also available.\\
For basic procedures to run FAMOUS version 4.5.3 on the QUEST cluster, look at RunningQuest. Here I put some notes from my own experience of running a copy of xcpsb [tcmia] (although these contain some repetition of the ‘Running Quest’ page to provide the contexts). Similar notes for running with reconfiguration are also available here.\\
For basic procedures to run FAMOUS version 4.5.3 on the QUEST cluster, look at RunningQuest. Here I put some notes from my own experience of running a copy of xcpsb [tcmia] (although these contain some repetition of the Running Quest page to provide the contexts). Similar notes for running with reconfiguration are also available here.\\
For basic procedures to run FAMOUS version 4.5.3 on the QUEST cluster, look at RunningQuest. Here I put some notes from my own experience of running a copy of xcpsb [tcmia] (although these contain some repetition of the ‘Running Quest’ page to provide the contexts). Similar notes for running with reconfiguration are also available here.\\
For basic procedures to run FAMOUS version 4.5.3 on the QUEST cluster, look at RunningQuest. Here I put some notes from my own experience of running a copy of xcpsb [tcmia] (although these contain some repetition of the ‘Running Quest’ page to provide the contexts). Similar notes for running with reconfiguration are also available here.\\
For basic procedures to run FAMOUS version 4.5.3 on the QUEST cluster, look at RunningQuest. Here I put some notes from my own experience of running a copy of xcpsb [tcmia] (although these contain some repetition of the ‘Running Quest’ page to provide the contexts).\\
For basic procedures to run FAMOUS version 4.5.3 on the QUEST cluster, look at RunningQuest. Here I put some notes from my own experience of running a copy of xcpsb [tcmia] (although these contain some repetition of the ‘Running Quest’ page to provide the contexts). Similar notes for running with reconfiguration are also available here.\\
OR press the [SUBMIT] button on UMUI. Yes, this works in my case.
OR press the [SUBMIT] button on UMUI. Yes, this works.
~/umui_runs/[jobid]−012345678/[jobid]000.o1234
;~/umui_runs/[jobid]−012345678/[jobid]000.o1234
;~/umui_runs/[jobid]−012345678/[jobid]000.o1234
;~/umui_runs/[jobid]−012345678/[jobid]000.o1234
;3. also see trouble shooting [5] 4–3\\
3. also see trouble shooting [5] 4-8\\
5. also see trouble shooting [5] 3–5\\
5. also see trouble shooting [5] 3-5\\
8. also see trouble shooting [5] 4-8\\
8. also see trouble shooting [5] 4-8\\
[5] trouble shooting\\
[1] environments on quest\\
[2] process\\
[3] Compile the job\\
[4] Run the job\\
8. also see trouble shooting [5] 4–8\\
8. also see trouble shooting [5] 4-8\\
3–4: If compilation fails for some reason [eg ‘library not found’], try doing the following on quest;
4–8: didn’t run and got error message in ~/umui_runs/[jobid]−012345678/[jobid]000.o1234
;
puma
to quest
(this )* THIS DOES NOT START THE RUN. GO TO THE NEXT STEP!!!
puma
to quest
and DOES NOT START THE RUN. GO TO THE NEXT STEP!!!1. Submit from puma
to quest
(this only copies the files over)\\
1. Under [Compile Options], select “Run from existing exec”
2. Under [Job resources and re-submission], select “qsub” (the top one)
3. Save, process, and post-process (see [2]−2)
4. Submit using the [SUBMIT] button or “umsubmit” (see [3]−4). I get messages like below but it turned out submission is actually working in spite of the messages.
qsub: invalid option — x qsub: invalid option — s usage: qsub [-a date_time] [-A account_string] [-b secs] [-c c[=<INTERVAL›] ] [-C directive_prefix] [-d path] [-D path] [-e path] [-h] [-I] [-j oe] [-k {oe}] [-l resource_list] [-m {abe}] [-M user_list] [-N jobname] [-o path] [-p priority] [-q queue] [-r y|n] [-S path] [-u user_list] [-X] [-W otherattributes=value…] [-v variable_list] [-V ] [-z] [script]
- Under [Compile Options], select “Run from existing exec”
- Under [Job resources and re-submission], select “qsub” (the top one)
- Save, process, and post-process (see [2]−2)
- Submit using the [SUBMIT] button or “umsubmit” (see [3]−4). I get the messages like below but it turned out submission is actually working in spite of the messages.
qsub: invalid option — x qsub: invalid option — s usage: qsub [-a date_time] [-A account_string] [-b secs] [-c c[=<INTERVAL›] ] [-C directive_prefix] [-d path] [-D path] [-e path] [-h] [-I] [-j oe] [-k {oe}] [-l resource_list] [-m {abe}] [-M user_list] [-N jobname] [-o path] [-p priority] [-q queue] [-r y|n] [-S path] [-u user_list] [-X] [-W otherattributes=value…] [-v variable_list] [-V ] [-z] [script]
- output file may or may not be created. if created it will also be ***.leave in quest:~/umui_out\\
puma
to quest
(this )\\
6. Submit to run\\
2. Submit to run\\
cd $HOME/umui_runs
ls -lrt
cd [jobid]−012345678
(go to the latest directory)
- on quest cd to the newest directory in ~/umui_runs
cd $HOME/umui_runs
ls -lrt
cd [jobid]−012345678
(go to the latest directory)
~um/bin/qsub-um qsubmit.quest#
(# = 1 or 2; look in the directory)
- submit the job with
~um/bin/qsub-um qsubmit.quest#
(# = 1 or 2; look in the directory)
~/umui_runs/[jobid]−012345678/[jobid]000.o1234
when the run completes in any way (finished or stopped due to error). This should contain information that would previously be contained in .leave
files.\\
- check the status of the run by typing;
7. check the status of the run by typing;
- output will be created as ~/umui_runs/[jobid]−012345678/[jobid]000.o1234
when the run completes. This should contain information that would previously be contained in .leave
files.\\
8. also see trouble shooting [5] 4–8\\
3. also see trouble shooting [5] 4–3
\\
4–3: didn’t run and got error message in ~/umui_runs/[jobid]−012345678/[jobid]000.o1234
;
4–8: didn’t run and got error message in ~/umui_runs/[jobid]−012345678/[jobid]000.o1234
;
- output will be created as ~/umui_runs/[jobid]−012345678/[jobid]000.o1234
. This should contain information that would previously be contained in .leave
files.\\
- output will be created as ~/umui_runs/[jobid]−012345678/[jobid]000.o1234
when the run completes. This should contain information that would previously be contained in .leave
files.\\
THIS DOES NOT START THE RUN. GO TO THE NEXT STEP!!!\\
* THIS DOES NOT START THE RUN. GO TO THE NEXT STEP!!!\\
###THIS DOES NOT START THE RUN. GO TO THE NEXT STEP!!!\\
THIS DOES NOT START THE RUN. GO TO THE NEXT STEP!!!\\
- Submit using the [SUBMIT] button or “umsubmit”. I get the messages like below but it turned out submission is actually working in spite of the messages.
- Submit using the [SUBMIT] button or “umsubmit” (see [3]−4). I get the messages like below but it turned out submission is actually working in spite of the messages.
- check the status of the run by typing;
- check the status of the run by typing;
- check the status of the run by typing;
qstat -u [userid]
\\
###THIS DOES NOT START THE RUN. GO TO THE NEXT STEP!!!\\
- Submit using the [SUBMIT] button or “umsubmit”\\
- Submit using the [SUBMIT] button or “umsubmit”. I get the messages like below but it turned out submission is actually working in spite of the messages.
qsub: invalid option — x qsub: invalid option — s usage: qsub [-a date_time] [-A account_string] [-b secs] [-c c[=<INTERVAL›] ] [-C directive_prefix] [-d path] [-D path] [-e path] [-h] [-I] [-j oe] [-k {oe}] [-l resource_list] [-m {abe}] [-M user_list] [-N jobname] [-o path] [-p priority] [-q queue] [-r y|n] [-S path] [-u user_list] [-X] [-W otherattributes=value…] [-v variable_list] [-V ] [-z] [script]
- compilation takes several minutes.
- output file will be created as ***.leave in quest:~/umui_out. This file will typically be of 150~250 KB when compilation finishes successfully.\\
- output file will be created as ***.leave in quest:~/umui_out. This file is typically of 150~250 KB if compilation is successful.
\\
- Under [Compile Options], select “Run from existing exec”.
- Under [Job resources and re-submission], select “qsub” (the top one).
- Submit using the [SUBMIT] button or “umsubmit”.\\
- Under [Compile Options], select “Run from existing exec”
- Under [Job resources and re-submission], select “qsub” (the top one)
- Save, process, and post-process (see [2]−2)
- Submit using the [SUBMIT] button or “umsubmit”\\
1. at first UMUI froze during processing. it was found that the following lines in my puma:~/.kshrc
were somehow disturbing the processing;
1. in my first attempts UMUI froze during processing. it was found that the following lines in my puma:~/.kshrc
were somehow disturbing the processing;
so I commented out these lines.\\
so I commented out these lines.
\\
2. Under “Job resources and re-submission”, select “at”.\\
2. Under “Job resources and re-submission”, select “at”\\
3. Submit;
~jeff/bin/umsubmit -h quest-hpc.bris.ac.uk -u [userid] -r scp [jobid]
OR press the [SUBMIT] button on UMUI. Yes, this works in my case.
3. Save, process, and post-process (see [2]−2)\\
4. Submit;
~jeff/bin/umsubmit -h quest-hpc.bris.ac.uk -u [userid] -r scp [jobid]
OR press the [SUBMIT] button on UMUI. Yes, this works in my case.
\\
4. also see trouble shooting [5] 3–5\\
5. also see trouble shooting [5] 3–5\\
For basic procedures to run FAMOUS version 4.5.3 on the QUEST cluster, look at RunningQuest. Here I put some notes from my own experience of running a copy of xcpsb [tcmia] (although these contain some repetition to provide the contexts).\\
For basic procedures to run FAMOUS version 4.5.3 on the QUEST cluster, look at RunningQuest. Here I put some notes from my own experience of running a copy of xcpsb [tcmia] (although these contain some repetition of the ‘Running Quest’ page to provide the contexts).\\
For basic procedures to run FAMOUS version 4.5.3 on the QUEST cluster, look at the FAMOUS Wiki [http://www.famous.ac.uk/index.php/Main/RunningQuest]. Here I put some notes from my own experience of running a copy of xcpsb [tcmia] (although these contain some repetition to provide the contexts).\\
For basic procedures to run FAMOUS version 4.5.3 on the QUEST cluster, look at RunningQuest. Here I put some notes from my own experience of running a copy of xcpsb [tcmia] (although these contain some repetition to provide the contexts).\\
For basic procedures to run FAMOUS version 4.5.3 on the QUEST cluster, look at the FAMOUS Wiki [http://www.famous.ac.uk/index.php/Main/RunningQuest]. Here I put some notes from my own experience of running a copy of xcpsb [tcmia] (although these contain some repetition to provide the contexts).
[1] environments on quest
1. Copy the setvars file to your home directory
cd $HOME
cp /exports/gpfsbig/um/PUM 64?/setvars $HOME
ln -s setvars setvars_4.5
2. Append to your .profile (or equivalent):
module add default-infiniband-pgi-251
. $HOME/setvars
3. also see trouble shooting [5] 4–3
[2] process
1. at first UMUI froze during processing. it was found that the following lines in my puma:~/.kshrc
were somehow disturbing the processing;
set prompt=“/% “
set history=250
set savehist=250
so I commented out these lines.
2. processing still didn’t go well and that was because of the post processing. I could avoid this problem by setting all post processing scripts to “N
” in [local post-processing scripts] in UMUI. (You could find out which one is disturbing the processing by turning on and off from one script to another and try processing, but it was found that I have to turn off all scripts in my case.) So now post processing needs to be done manually every time after processing.
/home/famous/bin/he_namelist_new_phase5 [jobid]
/home/famous/bin/vfdrift_pp.sh [jobid]
/home/famous/bin/quest_queue.sh [jobid]
[3] Compile the job
The compilation and the run must be done in separate stages.
1. In “Compile Options” in the UMUI, select “compile and build then stop”
2. Under “Job resources and re-submission”, select “at”.
3. Submit;
~jeff/bin/umsubmit -h quest-hpc.bris.ac.uk -u [userid] -r scp [jobid]
OR press the [SUBMIT] button on UMUI. Yes, this works in my case.
- output file will be created as ***.leave in quest:~/umui_out. This file is typically of 150~250 KB if compilation is successful.
4. also see trouble shooting [5] 3–5
[4] Run the job
1. Submit from puma
to quest
(this only copies the files over)
- Under [Compile Options], select “Run from existing exec”.
- Under [Job resources and re-submission], select “qsub” (the top one).
- Submit using the [SUBMIT] button or “umsubmit”.
- output file may or may not be created. if created it will also be ***.leave in quest:~/umui_out
***THIS DOES NOT START THE RUN. GO TO THE NEXT STEP.
2. Submit to run
- on quest cd to the newest directory in ~/umui_runs
cd $HOME/umui_runs
ls -lrt
cd [jobid]−012345678
(go to the latest directory)
- submit the job with
~um/bin/qsub-um qsubmit.quest#
(# = 1 or 2; look in the directory)
- output will be created as ~/umui_runs/[jobid]−012345678/[jobid]000.o1234
. This should contain information that would previously be contained in .leave
files.
3. also see trouble shooting [5] 4–3
[5] trouble shooting
3–4: If compilation fails for some reason [eg ‘library not found’], try doing the following on quest;
cd ~/umui_runs
(go to the latest directory)
ls -lrt
cd [jobid]−012345678
./qsubmit.quest# > qsubmit.out 2>&1
(# = 1 or 2; look in the directory)
output qsubmit.out
will be created. it contains what .leave
file would contain.
4–3: didn’t run and got error message in ~/umui_runs/[jobid]−012345678/[jobid]000.o1234
;
/var/spool/PBS/mom_priv/jobs/8357.master.SC: /exports/gpfsbig/home/[userid]/umui_runs/ [jobid]−012345678/SCRIPT[42]: .: /vn4.5/scripts/setglobalvars: not found
In “SCRIPT
” in the same directory, there are lines;
VN=4.5 # Model version number . $UMDIR/vn$VN/scripts/setglobalvars # set UI system variables
So the problem seems that UMDIR
is not given a value.
UMDIR
is set in quest:~/setvars
(which should be linked to /exports/gpfsbig/um/PUM 64?/setvars
) as “UMDIR=~um/PUM 64?/um
” and should be read by the shell through “. $HOME/setvars
” in quest:~/.profile
. However it wasn’t read for some reason.
So a line “. $HOME/.profile
” is added to quest:~/.bashrc
so bash reads .profile
. If other shell is used this line needs to be added to .kshrc
, .tcshrc
etc.
Whether this is working Ok can be checked by typing “echo $UMDIR
” on UNIX command line.