Re: [Users] Cactus build problems
On 20/08/14 14:58, Frank Loeffler wrote: > On Wed, Aug 20, 2014 at 02:53:24PM +0100, Ian Smith wrote: >> $ cat simfactory/mdb/machines/sumo.ini >> [generic] > > Change this to [sumo] - because then simfactory will know that this > machine's name is 'sumo'. > >> # Access to this machine >> hostname= generic.some.where >> aliaspattern= ^generic\.some\.where$ > > You should probably change this to match sumo as well. This way you > don't have to give the machine file for every command. > >> # Source tree management >> sourcebasedir = /home/@USER@ >> optionlist = generic.cfg >> submitscript= generic.sub >> runscript = generic.run > > The 'generic' option list is quite 'reduced'. It might make more sense > to use a more specific option list here (debian/ubuntu/...). > >> ppn = 2 # or more >> max-num-threads = 2 # or more >> num-threads = 2 # or more >> nodes = 1 > > This looks good, assuming this is a one machine with two cores. > > Frank > Hi Frank, I have now solved the problem, just trying to understand precisely what I did to fix it! It seems that I already had a machine file (not sure at what point it was created) but unfortunately I didn't notice it earlier: $ cat simfactory/mdb/machines/sumo.doitto.me.uk.ini [sumo.doitto.me.uk] # Machine description nickname= sumo.doitto.me.uk name= sumo.doitto.me.uk location= somewhere description = Whatever status = personal # Access to this machine hostname= sumo.doitto.me.uk aliaspattern= ^generic\.some\.where$ # Source tree management sourcebasedir = /opt/EinsteinToolkit optionlist = /opt/EinsteinToolkit/Cactus/simfactory/mdb/optionlists/debian.cfg submitscript= generic.sub runscript = /opt/EinsteinToolkit/Cactus/simfactory/mdb/runscripts/debian.sh make= make -j2 basedir = /home/ian/simulations ppn = 2 max-num-threads = 2 num-threads = 2 nodes = 1 submit = exec @SCRIPTFILE@ < /dev/null > /dev/null 2> /dev/null & echo $! getstatus = ps @JOB_ID@ stop= kill @JOB_ID@ submitpattern = (.*) statuspattern = "^ *@JOB_ID@ " queuedpattern = $^ runningpattern = ^ holdingpattern = $^ exechost= echo localhost exechostpattern = (.*) stdout = cat @SIMULATION_NAME@.out stderr = cat @SIMULATION_NAME@.err stdout-follow = tail -n 100 -f @SIMULATION_NAME@.out @SIMULATION_NAME@.err So I did a build with this file as the --mdb oarameter, and now the command I use is: ./simfactory/bin/sim submit static_tov --parfile=par/static_tov_small.par --walltime=8:0:0 ie. I am not specifying cores or machines for the simulation on the command line any more. This now seems to work on two cores! So, if I had seen the file earlier, I might have just got away with editing it. As it is I rebuilt simfactory with the proper file, I don't know if I needed to. I might just reinstall tomorrow to settle it, but for now I think I'll continue to try out the software . . . Thanks to everyone for your patience! Cheers, Ian. ___ Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users
Re: [Users] Cactus build problems
On Wed, Aug 20, 2014 at 02:53:24PM +0100, Ian Smith wrote: > $ cat simfactory/mdb/machines/sumo.ini > [generic] Change this to [sumo] - because then simfactory will know that this machine's name is 'sumo'. > # Access to this machine > hostname= generic.some.where > aliaspattern= ^generic\.some\.where$ You should probably change this to match sumo as well. This way you don't have to give the machine file for every command. > # Source tree management > sourcebasedir = /home/@USER@ > optionlist = generic.cfg > submitscript= generic.sub > runscript = generic.run The 'generic' option list is quite 'reduced'. It might make more sense to use a more specific option list here (debian/ubuntu/...). > ppn = 2 # or more > max-num-threads = 2 # or more > num-threads = 2 # or more > nodes = 1 This looks good, assuming this is a one machine with two cores. Frank signature.asc Description: Digital signature ___ Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users
Re: [Users] Cactus build problems
On Wed, Aug 20, 2014 at 02:47:12PM +0100, Ian Smith wrote: > ./simfactory/bin/sim build --thornlist=manifest/einsteintoolkit.th > --machine=simfactory/mdb/machines/sumo.ini > Error: retrieving Machine entry for Machine > simfactory/mdb/machines/sumo.ini: Machine I believe that. --machine takes a machine name as argument, not the file name to the machine ini file. > -rw-r--r-- 1 ian ian 1.1K Aug 20 14:27 simfactory/mdb/machines/sumo.ini The name is what the first line ([ ... ]) in the ini file shows. > ./simfactory/bin/sim build --thornlist=manifest/einsteintoolkit.th > --mdb=simfactory/mdb/machines/sumo.ini This would work, because here you skip the name->file lookup. > ./simfactory/bin/sim submit static_tov --machine=sumo > --parfile=par/static_tov_small.par --ppn=2 --procs=2 --walltime=8:0:0 > Error: retrieving Machine entry for Machine sumo: Machine sumo doesn't exist It would be interesting to see which name you have set in sumo.ini. Could you attach the file to an email to the list? Also, if the ini file is setup nicely, you shouldn't have to specify the name at all, because simfactory would look at what 'hostname' returns and try to "guess" where it is. So, please also tell us what 'hostname' on sumo returns. Frank signature.asc Description: Digital signature ___ Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users
Re: [Users] Cactus build problems
I forgot to list my machine file, sorry! $ cat simfactory/mdb/machines/sumo.ini [generic] # Machine description nickname= sumo name= Generic Machine location= somewhere description = Whatever status = personal # Access to this machine hostname= generic.some.where aliaspattern= ^generic\.some\.where$ # Source tree management sourcebasedir = /home/@USER@ optionlist = generic.cfg submitscript= generic.sub runscript = generic.run make= make -j2 basedir = /home/@USER@/simulations ppn = 2 # or more max-num-threads = 2 # or more num-threads = 2 # or more nodes = 1 submit = exec @SCRIPTFILE@ < /dev/null > /dev/null 2> /dev/null & echo $! getstatus = ps @JOB_ID@ stop= kill @JOB_ID@ submitpattern = (.*) statuspattern = "^ *@JOB_ID@ " queuedpattern = $^ runningpattern = ^ holdingpattern = $^ exechost= echo localhost exechostpattern = (.*) stdout = cat @SIMULATION_NAME@.out stderr = cat @SIMULATION_NAME@.err stdout-follow = tail -n 100 -f @SIMULATION_NAME@.out @SIMULATION_NAME@.err Cheers, Ian. ___ Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users
Re: [Users] Cactus build problems
On 20/08/14 13:56, Dumsani Ndzinisa wrote: > Hi Ian, > > As far as I know, those limits are set in the machine definition file, > the .ini file specifically. Once you have added them on, do a fresh > build, making sure to pass the ini file as an (optional) argument to > you new build. That is, simfactory/bin/sim build . > --machine=simfactory/mdb/machines/ > If not set, they will take on some default values which might limit > you on submission when you now try to ask for more cores > (processors) than the set (default) maximum. This seems to be > the trouble in your case. > > It is also possible for the ini file that you are currently using not to > have these variables. In that case, you will need to add them. See > an example ini file in the files shipped with the code (in > simfactory/mdb/machines/). > > I hope that helps shed some light. > > Regards, > Dumsani Hi Dumsani, Thanks for your help. I was confident that your suggestion would work, but would you believe this? ./simfactory/bin/sim build --thornlist=manifest/einsteintoolkit.th --machine=simfactory/mdb/machines/sumo.ini Error: retrieving Machine entry for Machine simfactory/mdb/machines/sumo.ini: Machine simfactory/mdb/machines/sumo.ini doesn't exist Aborting Simfactory. ls -lAh simfactory/mdb/machines/sumo.ini -rw-r--r-- 1 ian ian 1.1K Aug 20 14:27 simfactory/mdb/machines/sumo.ini So I looked in sim --help and tried: ./simfactory/bin/sim build --thornlist=manifest/einsteintoolkit.th --mdb=simfactory/mdb/machines/sumo.ini and that seemed to work, and ./simfactory/bin/sim submit static_tov --parfile=par/static_tov_small.par --walltime=8:0:0 started a process, but on one CPU as before. So I then tried: ./simfactory/bin/sim submit static_tov --machine=sumo --parfile=par/static_tov_small.par --ppn=2 --procs=2 --walltime=8:0:0 Error: retrieving Machine entry for Machine sumo: Machine sumo doesn't exist Aborting Simfactory. then I tried sumo.ini, path to sumo.ini (but I specified the machine for the build so do I need to do this in the sim command as well?) and probably a few other things, but still can't get more than one core/thread to start. Phew! Any other suggestions? Cheers, Ian. ___ Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users
Re: [Users] Cactus build problems
Hi Ian, As far as I know, those limits are set in the machine definition file, the .ini file specifically. Once you have added them on, do a fresh build, making sure to pass the ini file as an (optional) argument to you new build. That is, simfactory/bin/sim build . --machine=simfactory/mdb/machines/ If not set, they will take on some default values which might limit you on submission when you now try to ask for more cores (processors) than the set (default) maximum. This seems to be the trouble in your case. It is also possible for the ini file that you are currently using not to have these variables. In that case, you will need to add them. See an example ini file in the files shipped with the code (in simfactory/mdb/machines/). I hope that helps shed some light. Regards, Dumsani On 20/08/2014 14:35, Ian Smith wrote: > Hi Guys, > > I tried to run the resource-reduced example (static_tov_small.par) in > the simplified guide, but the simulation only uses one CPU core. I > tried a couple of things to fix this: > > ian@sumo Wed Aug 20 01:26 PM /opt/EinsteinToolkit/Cactus > $ ./simfactory/bin/sim submit static_tov > --parfile=par/static_tov_small.par --procs=2 --walltime=8:0:0 > Assigned restart id: 3 > Error: Too many nodes specified: nodes=2 (maxnodes is 1) > Aborting Simfactory. > > ian@sumo Wed Aug 20 01:27 PM /opt/EinsteinToolkit/Cactus > $ ./simfactory/bin/sim submit static_tov > --parfile=par/static_tov_small.par --ppn=2 --procs=2 --walltime=8:0:0 > Assigned restart id: 4 > Error: Illegal number of requested cores per node specified: specified > ppn=2 (min-ppn is 1, max-ppn is 1) > Aborting Simfactory. > > I can't see where these max & min limits are set, I checked in > simfactory/etc, can anyone enlighten me? > > Cheers, > > Ian. > > ___ > Users mailing list > Users@einsteintoolkit.org > http://lists.einsteintoolkit.org/mailman/listinfo/users ___ Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users
Re: [Users] Cactus build problems
Hi Guys, I tried to run the resource-reduced example (static_tov_small.par) in the simplified guide, but the simulation only uses one CPU core. I tried a couple of things to fix this: ian@sumo Wed Aug 20 01:26 PM /opt/EinsteinToolkit/Cactus $ ./simfactory/bin/sim submit static_tov --parfile=par/static_tov_small.par --procs=2 --walltime=8:0:0 Assigned restart id: 3 Error: Too many nodes specified: nodes=2 (maxnodes is 1) Aborting Simfactory. ian@sumo Wed Aug 20 01:27 PM /opt/EinsteinToolkit/Cactus $ ./simfactory/bin/sim submit static_tov --parfile=par/static_tov_small.par --ppn=2 --procs=2 --walltime=8:0:0 Assigned restart id: 4 Error: Illegal number of requested cores per node specified: specified ppn=2 (min-ppn is 1, max-ppn is 1) Aborting Simfactory. I can't see where these max & min limits are set, I checked in simfactory/etc, can anyone enlighten me? Cheers, Ian. ___ Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users
Re: [Users] Cactus build problems
[sorry to have to re-send this, Thunderbird is playing havoc with my From: address!] Hi again List, I tried again from scratch, in case I was building against artifacts created with incomplete dependencies (looks like I was). I got this: Formaline: Creating git master repository... Formaline: Creating git local repository... Formaline: Pushing source tree to master git repository... /usr/bin/ld: cannot find -lnuma /usr/bin/ld: cannot find -lltdl collect2: error: ld returned 1 exit status make[1]: *** [/opt/ET/Cactus/exe/cactus_sim] Error 1 make[1]: *** Waiting for unfinished jobs Formaline: Pushing to local repository /opt/ET/Cactus/../CactusSourceJar.git... Formaline: Optimising git repository (slow only the first time)... make: *** [sim] Error 2 I fixed it with a couple more dependencies (probably needed for Debian as well as Ubuntu): sudo apt-get install libnuma-dev libltdl-dev ian@bonsai Wed Aug 20 11:17 AM /opt/ET/Cactus $ ls -lAh exe total 291M -rwxrwxr-x 1 ian ian 291M Aug 20 11:16 cactus_sim drwxrwxr-x 2 ian ian 4.0K Aug 20 11:17 sim I think I've now got a system to try out . . . so thanks for the moral support guys! Cheers, Ian. ___ Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users
Re: [Users] Cactus build problems
On 18/08/14 18:20, Erik Schnetter wrote: > Ian > > Most likely, setting both F77 and F90 to "gfortran" will work. Thanks for the suggestion, Erik, I tried this, and still get the same error message. > You didn't specify what MPI options you are using when configuring. Can > you provide more details? I don't think I'm using MPI at all, what details would help? I've tried manual, Debian and Ubuntu configs and they all fail in the same way. Is it possible to clean the build, I couldn't see any option to do this? This is where I am now: -- There were 3 errors during execution of the CST These must be corrected before compilation can proceed -- -- Warnings were generated during execution of the CST -- CST error 1: -> Configuration script for thorn FORTRAN returned exit code 1 Error message: 'Fortran thorn requires that a Fortran compiler is defined, but F77 = 'none' and F90 = 'none'. Aborting.' CST error 2: -> Configuration script for thorn LORENE returned exit code 1 (no error message) CST error 3: -> Configuration script for thorn MPI returned exit code 1 (no error message) -- make[1]: *** [/opt/EinsteinToolkit/Cactus/configs/sim/config-data/make.thornlist] Error 1 make: *** [sim] Error 2 How do I make the system see3 my Fortran compilers? BTW the Wiki instructions themselves are simple and clear and easy to follow, they just don't seem to be sufficient to produce a working system. Cheers, Ian. ___ Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users
Re: [Users] Cactus build problems
On 19/08/14 17:42, Frank Loeffler wrote: > On Tue, Jul 29, 2014 at 03:57:00PM +0100, Ian Smith wrote: >> I've tried building this a few times over the last couple of years, on >> different machines, and always get stuck at the build stage, currently I >> have this set of errors: > >> $ aptitude search fort | grep '^i' >> i fort77 - Invoke f2c like a real compiler >> i gfortran- GNU Fortran 95 compiler > > This looks like a Debian, or Debian-like system. You could give the > debian option list a try: > > sim build --optionlist debian.cfg > > Or manually look at the option list first, for a list of suggested > packages, in simfactory/mdb/optionlists/debian.cfg > > Frank > Thanks to you and Erik for replying, I'll give it another go tomorrow, and try to provide more info if I can. Ian. PS sorry for replying personally, Frank, I haven't done mailing lists for a while! ___ Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users
Re: [Users] Cactus build problems
On Tue, Jul 29, 2014 at 03:57:00PM +0100, Ian Smith wrote: > I've tried building this a few times over the last couple of years, on > different machines, and always get stuck at the build stage, currently I > have this set of errors: > $ aptitude search fort | grep '^i' > i fort77 - Invoke f2c like a real compiler > i gfortran- GNU Fortran 95 compiler This looks like a Debian, or Debian-like system. You could give the debian option list a try: sim build --optionlist debian.cfg Or manually look at the option list first, for a list of suggested packages, in simfactory/mdb/optionlists/debian.cfg Frank signature.asc Description: Digital signature ___ Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users
Re: [Users] Cactus build problems
Ian Most likely, setting both F77 and F90 to "gfortran" will work. You didn't specify what MPI options you are using when configuring. Can you provide more details? -erik On Tue, Jul 29, 2014 at 10:57 AM, Ian Smith wrote: > Hi List! > > I've tried building this a few times over the last couple of years, on > different machines, and always get stuck at the build stage, currently I > have this set of errors: > > -- > There were 3 errors during execution of the CST > These must be corrected before compilation can proceed > -- > > -- > Warnings were generated during execution of the CST > -- > > CST error 1: >-> Configuration script for thorn FORTRAN returned exit code 1 > Error message: 'Fortran thorn requires that a Fortran compiler is > defined, but F77 = 'none' and F90 = 'none'. Aborting.' > > > CST error 2: >-> Configuration script for thorn LORENE returned exit code 1 > (no error message) > > > CST error 3: >-> Configuration script for thorn MPI returned exit code 1 > (no error message) > > -- > > I have all the compilers that I think are needed, and have also added > the dependencies listed at > https://docs.einsteintoolkit.org/et-docs/Simplified_Tutorial_for_New_Users > > I have also tried things like: > > export F77=/usr/bin/f77 > export F90=/usr/bin/f95 > > to no avail. As for installed packages, these seem relevant to the > errors . . . > > ian@bonsai Tue Jul 29 02:58 PM /opt/EinsteinToolkit/Cactus > $ aptitude search fort | grep '^i' > i fort77 - Invoke f2c like a real compiler > i gfortran- GNU Fortran 95 compiler > i A gfortran-4.8- GNU Fortran compiler > i A libgfortran-4.8-dev - Runtime library for GNU Fortran > applicatio > i libgfortran3- Runtime library for GNU Fortran > applicatio > ian@bonsai Tue Jul 29 02:58 PM /opt/EinsteinToolkit/Cactus > $ aptitude search mpi | grep '^i' > i libmpich-dev- Development files for MPICH > i A libmpich10 - Shared libraries for MPICH > i libmpich2-dev - Transitional dummy package for > MPICH devel > i A libopenmpi1.6 - high performance message passing > library - > i A mpi-default-bin - Standard MPI runtime programs > (metapackage > i A mpich - Implementation of the MPI Message > Passing > i mpich2 - Transitional dummy package > i A openmpi-bin - high performance message passing > library - > i A openmpi-common - high performance message passing > library - > > Can anyone assist with this? I am using Xubuntu 14.04 64-bit. > > Cheers, > > Ian. > > ___ > Users mailing list > Users@einsteintoolkit.org > http://lists.einsteintoolkit.org/mailman/listinfo/users > -- Erik Schnetter http://www.perimeterinstitute.ca/personal/eschnetter/ ___ Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users
