Changed line 54 from:
3. Save, process, and post-process (see [2]-2)\\
to:
3. Save, process, and post-process if necessary (see [2]-2)\\
Changed lines 73-74 from:
3. Save, process, and post-process (see [2]-2)\\
to:
3. Save, process, and post-process if necessary (see [2]-2)\\
Changed lines 38-39 from:
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.\\
to:
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.\\
Changed lines 38-39 from:
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.\\
to:
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.\\
Changed lines 26-27 from:
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;\\
to:
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;\\
Changed lines 31-45 from:
so I commented out these lines.\\
to:
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]
Changed lines 47-51 from:
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]
to:
!!!'''[-[3] Compile the job-]'''\\
Changed line 51 from:
!!!'''[-[3] Compile the job-]'''\\
to:
The compilation and the run must be done in separate stages.\\
Deleted lines 52-54:
The compilation and the run must be done in separate stages.\\
\\
Changed line 20 from:
3. also see trouble shooting [5] 4-3\\
to:
3. also see trouble shooting [[#ts48 | [5] 4-8]]\\
Changed line 58 from:
5. also see trouble shooting [5] 3-5\\
to:
5. also see trouble shooting [[#ts35 | [5] 3-5]]\\
Changed line 104 from:
8. also see trouble shooting [[#ts48 | [5] 4-8]]\\
to:
8. also see trouble shooting [[#ts48 | [5] 4-8]]\\
Changed line 110 from:
to:
Changed line 6 from:
!!!'''[1] environments on quest'''\\
to:
!!!'''[-[1] environments on quest-]'''\\
Added line 8:
Changed line 22 from:
to:
!!!'''[-[2] process-]'''\\
Added line 24:
Changed line 38 from:
!!!'''[3] Compile the job'''\\
to:
!!!'''[-[3] Compile the job-]'''\\
Added line 40:
Changed line 58 from:
!!!'''[4] Run the job'''\\
to:
!!!'''[-[4] Run the job-]'''\\
Added line 60:
Changed line 103 from:
'''[5] trouble shooting'''\\
to:
!!!'''[-[5] trouble shooting-]'''\\
Changed line 6 from:
'''[1] environments on quest'''\\
to:
!!!'''[1] environments on quest'''\\
Changed line 21 from:
to:
Changed line 36 from:
'''[3] Compile the job'''\\
to:
!!!'''[3] Compile the job'''\\
Changed line 55 from:
to:
!!!'''[4] Run the job'''\\
Changed line 97 from:
8. also see trouble shooting [5] 4-8\\
to:
8. also see trouble shooting [[#ts48 | [5] 4-8]]\\
Changed lines 101-102 from:
3-4: If compilation fails for some reason [eg 'library not found'], try doing the following on quest;\\
to:
[[#ts34]]
!!![-3-4: If compilation fails for some reason [eg 'library not found'], try doing the following on quest;-]\\
Changed lines 111-112 from:
4-8: didn't run and got error message in @@~/umui_runs/[jobid]-012345678/[jobid]000.o1234@@;\\
to:
[[#ts48]]
!!!4-8: didn't run and got error message in @@~/umui_runs/[jobid]-012345678/[jobid]000.o1234@@;\\
Changed lines 57-72 from:
1. Submit from @@puma@@ to @@quest@@ (this only copies the files over)\\
to:
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>] | s | n }] [-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]
Changed lines 74-91 from:
- 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>] | s | n }] [-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\\
to:
* this only copies the files from @@puma@@ to @@quest@@ (this )\\
Added lines 76-77:
* output file doesn't seem to be created.\\
\\
Added lines 79-80:
Changed lines 82-86 from:
to:
* on quest cd to the newest directory in ~/umui_runs\\
@@cd $HOME/umui_runs\\
ls -lrt\\
cd [jobid]-012345678@@ (go to the latest directory)
Changed lines 88-92 from:
- on quest cd to the newest directory in ~umui_runs\\
@@cd $HOME/umui_runs\\
ls -lrt\\
cd [jobid]-012345678@@ (go to the latest directory)
to:
* submit the job with\\
@@~um/bin/qsub-um qsubmit.quest#@@ (# = 1 or 2; look in the directory)
Changed lines 92-94 from:
- submit the job with\\
@@~um/bin/qsub-um qsubmit.quest#@@ (# = 1 or 2; look in the directory)
to:
* output will be created as @@~/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.\\
Changed lines 94-95 from:
- check the status of the run by typing;\\
to:
7. check the status of the run by typing;\\
Changed lines 98-99 from:
- 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.\\
to:
8. also see trouble shooting [5] 4-8\\
Deleted lines 100-101:
3. also see trouble shooting [5] 4-3\\
\\
Changed lines 112-113 from:
4-3: didn't run and got error message in @@~/umui_runs/[jobid]-012345678/[jobid]000.o1234@@;\\
to:
4-8: didn't run and got error message in @@~/umui_runs/[jobid]-012345678/[jobid]000.o1234@@;\\
Added line 60:
Added line 62:
Changed lines 64-75 from:
- Submit using the [SUBMIT] button or "umsubmit"\\
to:
- 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>] | s | n }] [-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]
Changed line 78 from:
***THIS DOES NOT START THE RUN. GO TO THE NEXT STEP.\\
to:
###THIS DOES NOT START THE RUN. GO TO THE NEXT STEP.\\
Changed lines 59-61 from:
- 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".\\
to:
- 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"\\
Changed lines 23-24 from:
1. at first UMUI froze during processing. it was found that the following lines in my @@puma:~/.kshrc@@ were somehow disturbing the processing;\\
to:
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;\\
Added lines 28-29:
so I commented out these lines.\\
Deleted lines 30-31:
so I commented out these lines.\\
\\
Changed line 43 from:
2. Under "Job resources and re-submission", select "at".\\
to:
2. Under "Job resources and re-submission", select "at"\\
Changed lines 45-48 from:
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.
to:
3. Save, process, and post-process (see [2]-2)\\
Added lines 47-51:
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.
\\
Changed line 54 from:
4. also see trouble shooting [5] 3-5\\
to:
5. also see trouble shooting [5] 3-5\\
Added lines 1-106:
!!! '''[+Notes from running FAMOUS ver. 4.5.3 on QUEST+]'''
\\
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/PUM64/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="%m:%/% "\\
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\\
ls -lrt\\
cd [jobid]-012345678@@ (go to the latest directory)\\
@@./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/PUM64/setvars@@) as "@@UMDIR=~um/PUM64/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.