[OMPI users] Java binding requirements
Hi, Recently, I tried to use Java bindings in Open MPI released this February. As far as mentioned in the Java FAQ ( http://www.open-mpi.org/faq/?category=java ), the Java binding implementation doesn't cause any performance degradation because of just wrapping native Open MPI with mpiJava-based APIs. I believe this means no Java code is required to run on all processing nodes (workers) but it has only to run on a master node. Is this understanding correct? If so, my question is if I need NOT to install JDK to the all nodes. In other words is it possible to have a machine used as a worker without JDK installed? Thanks a lot for any comment in advance. Regards, --yoshiki
[OMPI users] ompi-clean on single executable
Hi all, I am having issue running ompi-clean which clean up (this is normal) session associated to a user which means it kills all running jobs assoicated to this session (this is also normal). But I would like to be able to clean up session associated to a job (a not user). Here is my point: I am running two executable : % mpirun -np 2 myexec1 --> run with PID 2399 ... % mpirun -np 2 myexec2 --> run with PID 2402 ... When I run orte-clean I got this result : % orte-clean -v orte-clean: cleaning session dir tree openmpi-sessions-ndelader@myhost_0 orte-clean: killing any lingering procs orte-clean: found potential rogue orterun process (pid=2399,user=ndelader), sending SIGKILL... orte-clean: found potential rogue orterun process (pid=2402,user=ndelader), sending SIGKILL... Which means that both jobs have been killed :-( Basically I would like to perform orte-clean using executable name or PID or whatever that identify which job I want to stop an clean. It seems I would need to create an openmpi session per job. Does it make sense ? And I would like to be able to do something like following command and get following result : % orte-clean -v myexec1 orte-clean: cleaning session dir tree openmpi-sessions-ndelader@myhost_0 orte-clean: killing any lingering procs orte-clean: found potential rogue orterun process (pid=2399,user=ndelader), sending SIGKILL... Does it make sense ? Is there a way to perform this kind of selection in cleaning process ? Regards, Nicolas
Re: [OMPI users] ompi-clean on single executable
Hi, Am 24.10.2012 um 09:36 schrieb Nicolas Deladerriere: > I am having issue running ompi-clean which clean up (this is normal) session > associated to a user which means it kills all running jobs assoicated to this > session (this is also normal). But I would like to be able to clean up > session associated to a job (a not user). > > Here is my point: > > I am running two executable : > > % mpirun -np 2 myexec1 >--> run with PID 2399 ... > % mpirun -np 2 myexec2 >--> run with PID 2402 ... > > When I run orte-clean I got this result : > % orte-clean -v > orte-clean: cleaning session dir tree openmpi-sessions-ndelader@myhost_0 > orte-clean: killing any lingering procs > orte-clean: found potential rogue orterun process (pid=2399,user=ndelader), > sending SIGKILL... > orte-clean: found potential rogue orterun process (pid=2402,user=ndelader), > sending SIGKILL... > > Which means that both jobs have been killed :-( > Basically I would like to perform orte-clean using executable name or PID or > whatever that identify which job I want to stop an clean. It seems I would > need to create an openmpi session per job. Does it make sense ? And I would > like to be able to do something like following command and get following > result : > > % orte-clean -v myexec1 > orte-clean: cleaning session dir tree openmpi-sessions-ndelader@myhost_0 > orte-clean: killing any lingering procs > orte-clean: found potential rogue orterun process (pid=2399,user=ndelader), > sending SIGKILL... > > > Does it make sense ? Is there a way to perform this kind of selection in > cleaning process ? How many jobs are you starting on how many nodes at one time? This requirement could be a point to start to use a queuing system, where can remove job individually and also serialize your workflow. In fact: we use GridEngine also local on workstations for this purpose. -- Reuti
Re: [OMPI users] ompi-clean on single executable
Reuti, Thanks for your comments, In our case, we are currently running different mpirun commands on clusters sharing the same frontend. Basically we use a wrapper to run the mpirun command and to run an ompi-clean command to clean up the mpi job if required. Using ompi-clean like this just kills all other mpi jobs running on same frontend. I cannot use queuing system as you have suggested this is why I was wondering a option or other solution associated to ompi-clean command to avoid this general mpi jobs cleaning. Cheers Nicolas 2012/10/24, Reuti : > Hi, > > Am 24.10.2012 um 09:36 schrieb Nicolas Deladerriere: > >> I am having issue running ompi-clean which clean up (this is normal) >> session associated to a user which means it kills all running jobs >> assoicated to this session (this is also normal). But I would like to be >> able to clean up session associated to a job (a not user). >> >> Here is my point: >> >> I am running two executable : >> >> % mpirun -np 2 myexec1 >>--> run with PID 2399 ... >> % mpirun -np 2 myexec2 >>--> run with PID 2402 ... >> >> When I run orte-clean I got this result : >> % orte-clean -v >> orte-clean: cleaning session dir tree openmpi-sessions-ndelader@myhost_0 >> orte-clean: killing any lingering procs >> orte-clean: found potential rogue orterun process >> (pid=2399,user=ndelader), sending SIGKILL... >> orte-clean: found potential rogue orterun process >> (pid=2402,user=ndelader), sending SIGKILL... >> >> Which means that both jobs have been killed :-( >> Basically I would like to perform orte-clean using executable name or PID >> or whatever that identify which job I want to stop an clean. It seems I >> would need to create an openmpi session per job. Does it make sense ? And >> I would like to be able to do something like following command and get >> following result : >> >> % orte-clean -v myexec1 >> orte-clean: cleaning session dir tree openmpi-sessions-ndelader@myhost_0 >> orte-clean: killing any lingering procs >> orte-clean: found potential rogue orterun process >> (pid=2399,user=ndelader), sending SIGKILL... >> >> >> Does it make sense ? Is there a way to perform this kind of selection in >> cleaning process ? > > How many jobs are you starting on how many nodes at one time? This > requirement could be a point to start to use a queuing system, where can > remove job individually and also serialize your workflow. In fact: we use > GridEngine also local on workstations for this purpose. > > -- Reuti > ___ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users >
Re: [OMPI users] ompi-clean on single executable
Am 24.10.2012 um 11:33 schrieb Nicolas Deladerriere: > Reuti, > > Thanks for your comments, > > In our case, we are currently running different mpirun commands on > clusters sharing the same frontend. Basically we use a wrapper to run > the mpirun command and to run an ompi-clean command to clean up the > mpi job if required. > Using ompi-clean like this just kills all other mpi jobs running on > same frontend. I cannot use queuing system Why? Using it on a single machine was only one possible setup. Its purpose is to distribute jobs to slave hosts. If you have already one frontend as login-machine it fits perfect: the qmaster (in case of SGE) can run there and the execd on the nodes. -- Reuti > as you have suggested this > is why I was wondering a option or other solution associated to > ompi-clean command to avoid this general mpi jobs cleaning. > > Cheers > Nicolas > > 2012/10/24, Reuti : >> Hi, >> >> Am 24.10.2012 um 09:36 schrieb Nicolas Deladerriere: >> >>> I am having issue running ompi-clean which clean up (this is normal) >>> session associated to a user which means it kills all running jobs >>> assoicated to this session (this is also normal). But I would like to be >>> able to clean up session associated to a job (a not user). >>> >>> Here is my point: >>> >>> I am running two executable : >>> >>> % mpirun -np 2 myexec1 >>> --> run with PID 2399 ... >>> % mpirun -np 2 myexec2 >>> --> run with PID 2402 ... >>> >>> When I run orte-clean I got this result : >>> % orte-clean -v >>> orte-clean: cleaning session dir tree openmpi-sessions-ndelader@myhost_0 >>> orte-clean: killing any lingering procs >>> orte-clean: found potential rogue orterun process >>> (pid=2399,user=ndelader), sending SIGKILL... >>> orte-clean: found potential rogue orterun process >>> (pid=2402,user=ndelader), sending SIGKILL... >>> >>> Which means that both jobs have been killed :-( >>> Basically I would like to perform orte-clean using executable name or PID >>> or whatever that identify which job I want to stop an clean. It seems I >>> would need to create an openmpi session per job. Does it make sense ? And >>> I would like to be able to do something like following command and get >>> following result : >>> >>> % orte-clean -v myexec1 >>> orte-clean: cleaning session dir tree openmpi-sessions-ndelader@myhost_0 >>> orte-clean: killing any lingering procs >>> orte-clean: found potential rogue orterun process >>> (pid=2399,user=ndelader), sending SIGKILL... >>> >>> >>> Does it make sense ? Is there a way to perform this kind of selection in >>> cleaning process ? >> >> How many jobs are you starting on how many nodes at one time? This >> requirement could be a point to start to use a queuing system, where can >> remove job individually and also serialize your workflow. In fact: we use >> GridEngine also local on workstations for this purpose. >> >> -- Reuti >> ___ >> users mailing list >> us...@open-mpi.org >> http://www.open-mpi.org/mailman/listinfo.cgi/users >> > ___ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users
Re: [OMPI users] ompi-clean on single executable
Reuti, The problem I am facing is a small small part of our production system, and I cannot modify our mpirun submission system. This is why i am looking at solution using only ompi-clean of mpirun command specification. Thanks, Nicolas 2012/10/24, Reuti : > Am 24.10.2012 um 11:33 schrieb Nicolas Deladerriere: > >> Reuti, >> >> Thanks for your comments, >> >> In our case, we are currently running different mpirun commands on >> clusters sharing the same frontend. Basically we use a wrapper to run >> the mpirun command and to run an ompi-clean command to clean up the >> mpi job if required. >> Using ompi-clean like this just kills all other mpi jobs running on >> same frontend. I cannot use queuing system > > Why? Using it on a single machine was only one possible setup. Its purpose > is to distribute jobs to slave hosts. If you have already one frontend as > login-machine it fits perfect: the qmaster (in case of SGE) can run there > and the execd on the nodes. > > -- Reuti > > >> as you have suggested this >> is why I was wondering a option or other solution associated to >> ompi-clean command to avoid this general mpi jobs cleaning. >> >> Cheers >> Nicolas >> >> 2012/10/24, Reuti : >>> Hi, >>> >>> Am 24.10.2012 um 09:36 schrieb Nicolas Deladerriere: >>> I am having issue running ompi-clean which clean up (this is normal) session associated to a user which means it kills all running jobs assoicated to this session (this is also normal). But I would like to be able to clean up session associated to a job (a not user). Here is my point: I am running two executable : % mpirun -np 2 myexec1 --> run with PID 2399 ... % mpirun -np 2 myexec2 --> run with PID 2402 ... When I run orte-clean I got this result : % orte-clean -v orte-clean: cleaning session dir tree openmpi-sessions-ndelader@myhost_0 orte-clean: killing any lingering procs orte-clean: found potential rogue orterun process (pid=2399,user=ndelader), sending SIGKILL... orte-clean: found potential rogue orterun process (pid=2402,user=ndelader), sending SIGKILL... Which means that both jobs have been killed :-( Basically I would like to perform orte-clean using executable name or PID or whatever that identify which job I want to stop an clean. It seems I would need to create an openmpi session per job. Does it make sense ? And I would like to be able to do something like following command and get following result : % orte-clean -v myexec1 orte-clean: cleaning session dir tree openmpi-sessions-ndelader@myhost_0 orte-clean: killing any lingering procs orte-clean: found potential rogue orterun process (pid=2399,user=ndelader), sending SIGKILL... Does it make sense ? Is there a way to perform this kind of selection in cleaning process ? >>> >>> How many jobs are you starting on how many nodes at one time? This >>> requirement could be a point to start to use a queuing system, where can >>> remove job individually and also serialize your workflow. In fact: we >>> use >>> GridEngine also local on workstations for this purpose. >>> >>> -- Reuti >>> ___ >>> users mailing list >>> us...@open-mpi.org >>> http://www.open-mpi.org/mailman/listinfo.cgi/users >>> >> ___ >> users mailing list >> us...@open-mpi.org >> http://www.open-mpi.org/mailman/listinfo.cgi/users > > > ___ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users >
Re: [OMPI users] Java binding requirements
On Oct 23, 2012, at 9:51 PM, Yoshiki SATO wrote: > Hi, > > Recently, I tried to use Java bindings in Open MPI released this February. > As far as mentioned in the Java FAQ ( > http://www.open-mpi.org/faq/?category=java ), the Java binding implementation > doesn't cause any performance degradation because of just wrapping native > Open MPI with mpiJava-based APIs. I believe this means no Java code is > required to run on all processing nodes (workers) but it has only to run on a > master node. Is this understanding correct? Not sure I fully understand, but I believe the answer is no - Java code is going to run on all nodes where there are processes. > > If so, my question is if I need NOT to install JDK to the all nodes. In > other words is it possible to have a machine used as a worker without JDK > installed? > You do not need JDK installed on worker nodes - it only has to be on the node where you compile your code. However, we launch a JVM for each process, so you must at least have the JVM installed on each worker. This is typically included in a base Linux installation (just look for the "java" command, usually in /usr/bin), so you usually don't have to do anything special (as opposed to installing the JDK, which doesn't usually come in the base install) HTH Ralph > Thanks a lot for any comment in advance. > > Regards, > --yoshiki > ___ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users
Re: [OMPI users] ompi-clean on single executable
All things are possible, including what you describe. Not sure when we would get to it, though. On Oct 24, 2012, at 4:01 AM, Nicolas Deladerriere wrote: > Reuti, > > The problem I am facing is a small small part of our production > system, and I cannot modify our mpirun submission system. This is why > i am looking at solution using only ompi-clean of mpirun command > specification. > > Thanks, > Nicolas > > 2012/10/24, Reuti : >> Am 24.10.2012 um 11:33 schrieb Nicolas Deladerriere: >> >>> Reuti, >>> >>> Thanks for your comments, >>> >>> In our case, we are currently running different mpirun commands on >>> clusters sharing the same frontend. Basically we use a wrapper to run >>> the mpirun command and to run an ompi-clean command to clean up the >>> mpi job if required. >>> Using ompi-clean like this just kills all other mpi jobs running on >>> same frontend. I cannot use queuing system >> >> Why? Using it on a single machine was only one possible setup. Its purpose >> is to distribute jobs to slave hosts. If you have already one frontend as >> login-machine it fits perfect: the qmaster (in case of SGE) can run there >> and the execd on the nodes. >> >> -- Reuti >> >> >>> as you have suggested this >>> is why I was wondering a option or other solution associated to >>> ompi-clean command to avoid this general mpi jobs cleaning. >>> >>> Cheers >>> Nicolas >>> >>> 2012/10/24, Reuti : Hi, Am 24.10.2012 um 09:36 schrieb Nicolas Deladerriere: > I am having issue running ompi-clean which clean up (this is normal) > session associated to a user which means it kills all running jobs > assoicated to this session (this is also normal). But I would like to > be > able to clean up session associated to a job (a not user). > > Here is my point: > > I am running two executable : > > % mpirun -np 2 myexec1 > --> run with PID 2399 ... > % mpirun -np 2 myexec2 > --> run with PID 2402 ... > > When I run orte-clean I got this result : > % orte-clean -v > orte-clean: cleaning session dir tree > openmpi-sessions-ndelader@myhost_0 > orte-clean: killing any lingering procs > orte-clean: found potential rogue orterun process > (pid=2399,user=ndelader), sending SIGKILL... > orte-clean: found potential rogue orterun process > (pid=2402,user=ndelader), sending SIGKILL... > > Which means that both jobs have been killed :-( > Basically I would like to perform orte-clean using executable name or > PID > or whatever that identify which job I want to stop an clean. It seems I > would need to create an openmpi session per job. Does it make sense ? > And > I would like to be able to do something like following command and get > following result : > > % orte-clean -v myexec1 > orte-clean: cleaning session dir tree > openmpi-sessions-ndelader@myhost_0 > orte-clean: killing any lingering procs > orte-clean: found potential rogue orterun process > (pid=2399,user=ndelader), sending SIGKILL... > > > Does it make sense ? Is there a way to perform this kind of selection > in > cleaning process ? How many jobs are you starting on how many nodes at one time? This requirement could be a point to start to use a queuing system, where can remove job individually and also serialize your workflow. In fact: we use GridEngine also local on workstations for this purpose. -- Reuti ___ users mailing list us...@open-mpi.org http://www.open-mpi.org/mailman/listinfo.cgi/users >>> ___ >>> users mailing list >>> us...@open-mpi.org >>> http://www.open-mpi.org/mailman/listinfo.cgi/users >> >> >> ___ >> users mailing list >> us...@open-mpi.org >> http://www.open-mpi.org/mailman/listinfo.cgi/users >> > ___ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users
Re: [OMPI users] ompi-clean on single executable
...but patches would be greatly appreciated. :-) On Oct 24, 2012, at 12:24 PM, Ralph Castain wrote: > All things are possible, including what you describe. Not sure when we would > get to it, though. > > > On Oct 24, 2012, at 4:01 AM, Nicolas Deladerriere > wrote: > >> Reuti, >> >> The problem I am facing is a small small part of our production >> system, and I cannot modify our mpirun submission system. This is why >> i am looking at solution using only ompi-clean of mpirun command >> specification. >> >> Thanks, >> Nicolas >> >> 2012/10/24, Reuti : >>> Am 24.10.2012 um 11:33 schrieb Nicolas Deladerriere: >>> Reuti, Thanks for your comments, In our case, we are currently running different mpirun commands on clusters sharing the same frontend. Basically we use a wrapper to run the mpirun command and to run an ompi-clean command to clean up the mpi job if required. Using ompi-clean like this just kills all other mpi jobs running on same frontend. I cannot use queuing system >>> >>> Why? Using it on a single machine was only one possible setup. Its purpose >>> is to distribute jobs to slave hosts. If you have already one frontend as >>> login-machine it fits perfect: the qmaster (in case of SGE) can run there >>> and the execd on the nodes. >>> >>> -- Reuti >>> >>> as you have suggested this is why I was wondering a option or other solution associated to ompi-clean command to avoid this general mpi jobs cleaning. Cheers Nicolas 2012/10/24, Reuti : > Hi, > > Am 24.10.2012 um 09:36 schrieb Nicolas Deladerriere: > >> I am having issue running ompi-clean which clean up (this is normal) >> session associated to a user which means it kills all running jobs >> assoicated to this session (this is also normal). But I would like to >> be >> able to clean up session associated to a job (a not user). >> >> Here is my point: >> >> I am running two executable : >> >> % mpirun -np 2 myexec1 >> --> run with PID 2399 ... >> % mpirun -np 2 myexec2 >> --> run with PID 2402 ... >> >> When I run orte-clean I got this result : >> % orte-clean -v >> orte-clean: cleaning session dir tree >> openmpi-sessions-ndelader@myhost_0 >> orte-clean: killing any lingering procs >> orte-clean: found potential rogue orterun process >> (pid=2399,user=ndelader), sending SIGKILL... >> orte-clean: found potential rogue orterun process >> (pid=2402,user=ndelader), sending SIGKILL... >> >> Which means that both jobs have been killed :-( >> Basically I would like to perform orte-clean using executable name or >> PID >> or whatever that identify which job I want to stop an clean. It seems I >> would need to create an openmpi session per job. Does it make sense ? >> And >> I would like to be able to do something like following command and get >> following result : >> >> % orte-clean -v myexec1 >> orte-clean: cleaning session dir tree >> openmpi-sessions-ndelader@myhost_0 >> orte-clean: killing any lingering procs >> orte-clean: found potential rogue orterun process >> (pid=2399,user=ndelader), sending SIGKILL... >> >> >> Does it make sense ? Is there a way to perform this kind of selection >> in >> cleaning process ? > > How many jobs are you starting on how many nodes at one time? This > requirement could be a point to start to use a queuing system, where can > remove job individually and also serialize your workflow. In fact: we > use > GridEngine also local on workstations for this purpose. > > -- Reuti > ___ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users > ___ users mailing list us...@open-mpi.org http://www.open-mpi.org/mailman/listinfo.cgi/users >>> >>> >>> ___ >>> users mailing list >>> us...@open-mpi.org >>> http://www.open-mpi.org/mailman/listinfo.cgi/users >>> >> ___ >> users mailing list >> us...@open-mpi.org >> http://www.open-mpi.org/mailman/listinfo.cgi/users > > > ___ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users -- Jeff Squyres jsquy...@cisco.com For corporate legal information go to: http://www.cisco.com/web/about/doing_business/legal/cri/
Re: [OMPI users] ompi-clean on single executable
And just to give a little context, ompi-clean was created initially to "clean" up a node, not for cleaning up a specific job. It was for the case where MPI jobs would leave some files behind or leave some processes running. (I do not believe this happens much at all anymore.) But, as was said, no reason it could not be modified. >-Original Message- >From: users-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org] >On Behalf Of Jeff Squyres >Sent: Wednesday, October 24, 2012 12:56 PM >To: Open MPI Users >Subject: Re: [OMPI users] ompi-clean on single executable > >...but patches would be greatly appreciated. :-) > >On Oct 24, 2012, at 12:24 PM, Ralph Castain wrote: > >> All things are possible, including what you describe. Not sure when we >would get to it, though. >> >> >> On Oct 24, 2012, at 4:01 AM, Nicolas Deladerriere > wrote: >> >>> Reuti, >>> >>> The problem I am facing is a small small part of our production >>> system, and I cannot modify our mpirun submission system. This is why >>> i am looking at solution using only ompi-clean of mpirun command >>> specification. >>> >>> Thanks, >>> Nicolas >>> >>> 2012/10/24, Reuti : Am 24.10.2012 um 11:33 schrieb Nicolas Deladerriere: > Reuti, > > Thanks for your comments, > > In our case, we are currently running different mpirun commands on > clusters sharing the same frontend. Basically we use a wrapper to > run the mpirun command and to run an ompi-clean command to clean >up > the mpi job if required. > Using ompi-clean like this just kills all other mpi jobs running on > same frontend. I cannot use queuing system Why? Using it on a single machine was only one possible setup. Its purpose is to distribute jobs to slave hosts. If you have already one frontend as login-machine it fits perfect: the qmaster (in case of SGE) can run there and the execd on the nodes. -- Reuti > as you have suggested this > is why I was wondering a option or other solution associated to > ompi-clean command to avoid this general mpi jobs cleaning. > > Cheers > Nicolas > > 2012/10/24, Reuti : >> Hi, >> >> Am 24.10.2012 um 09:36 schrieb Nicolas Deladerriere: >> >>> I am having issue running ompi-clean which clean up (this is >>> normal) session associated to a user which means it kills all >>> running jobs assoicated to this session (this is also normal). >>> But I would like to be able to clean up session associated to a >>> job (a not user). >>> >>> Here is my point: >>> >>> I am running two executable : >>> >>> % mpirun -np 2 myexec1 >>> --> run with PID 2399 ... >>> % mpirun -np 2 myexec2 >>> --> run with PID 2402 ... >>> >>> When I run orte-clean I got this result : >>> % orte-clean -v >>> orte-clean: cleaning session dir tree >>> openmpi-sessions-ndelader@myhost_0 >>> orte-clean: killing any lingering procs >>> orte-clean: found potential rogue orterun process >>> (pid=2399,user=ndelader), sending SIGKILL... >>> orte-clean: found potential rogue orterun process >>> (pid=2402,user=ndelader), sending SIGKILL... >>> >>> Which means that both jobs have been killed :-( Basically I would >>> like to perform orte-clean using executable name or PID or >>> whatever that identify which job I want to stop an clean. It >>> seems I would need to create an openmpi session per job. Does it >make sense ? >>> And >>> I would like to be able to do something like following command >>> and get following result : >>> >>> % orte-clean -v myexec1 >>> orte-clean: cleaning session dir tree >>> openmpi-sessions-ndelader@myhost_0 >>> orte-clean: killing any lingering procs >>> orte-clean: found potential rogue orterun process >>> (pid=2399,user=ndelader), sending SIGKILL... >>> >>> >>> Does it make sense ? Is there a way to perform this kind of >>> selection in cleaning process ? >> >> How many jobs are you starting on how many nodes at one time? This >> requirement could be a point to start to use a queuing system, >> where can remove job individually and also serialize your >> workflow. In fact: we use GridEngine also local on workstations >> for this purpose. >> >> -- Reuti >> ___ >> users mailing list >> us...@open-mpi.org >> http://www.open-mpi.org/mailman/listinfo.cgi/users >> > ___ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users ___ users mailing list us...@open-mpi.org http://www.open-mpi.org/mailman/listinfo.cgi/users >>> ___ >>> users m
Re: [OMPI users] ompi-clean on single executable
Or perhaps cloned, renamed to orte-kill, and modified to kill a single (or
multiple) specific job(s). That would be POSIX-like ("kill" vs. "clean").
On Oct 24, 2012, at 1:32 PM, Rolf vandeVaart wrote:
> And just to give a little context, ompi-clean was created initially to
> "clean" up a node, not for cleaning up a specific job. It was for the case
> where MPI jobs would leave some files behind or leave some processes running.
> (I do not believe this happens much at all anymore.) But, as was said, no
> reason it could not be modified.
>
>> -Original Message-
>> From: users-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org]
>> On Behalf Of Jeff Squyres
>> Sent: Wednesday, October 24, 2012 12:56 PM
>> To: Open MPI Users
>> Subject: Re: [OMPI users] ompi-clean on single executable
>>
>> ...but patches would be greatly appreciated. :-)
>>
>> On Oct 24, 2012, at 12:24 PM, Ralph Castain wrote:
>>
>>> All things are possible, including what you describe. Not sure when we
>> would get to it, though.
>>>
>>>
>>> On Oct 24, 2012, at 4:01 AM, Nicolas Deladerriere
>> wrote:
>>>
Reuti,
The problem I am facing is a small small part of our production
system, and I cannot modify our mpirun submission system. This is why
i am looking at solution using only ompi-clean of mpirun command
specification.
Thanks,
Nicolas
2012/10/24, Reuti :
> Am 24.10.2012 um 11:33 schrieb Nicolas Deladerriere:
>
>> Reuti,
>>
>> Thanks for your comments,
>>
>> In our case, we are currently running different mpirun commands on
>> clusters sharing the same frontend. Basically we use a wrapper to
>> run the mpirun command and to run an ompi-clean command to clean
>> up
>> the mpi job if required.
>> Using ompi-clean like this just kills all other mpi jobs running on
>> same frontend. I cannot use queuing system
>
> Why? Using it on a single machine was only one possible setup. Its
> purpose is to distribute jobs to slave hosts. If you have already
> one frontend as login-machine it fits perfect: the qmaster (in case
> of SGE) can run there and the execd on the nodes.
>
> -- Reuti
>
>
>> as you have suggested this
>> is why I was wondering a option or other solution associated to
>> ompi-clean command to avoid this general mpi jobs cleaning.
>>
>> Cheers
>> Nicolas
>>
>> 2012/10/24, Reuti :
>>> Hi,
>>>
>>> Am 24.10.2012 um 09:36 schrieb Nicolas Deladerriere:
>>>
I am having issue running ompi-clean which clean up (this is
normal) session associated to a user which means it kills all
running jobs assoicated to this session (this is also normal).
But I would like to be able to clean up session associated to a
job (a not user).
Here is my point:
I am running two executable :
% mpirun -np 2 myexec1
--> run with PID 2399 ...
% mpirun -np 2 myexec2
--> run with PID 2402 ...
When I run orte-clean I got this result :
% orte-clean -v
orte-clean: cleaning session dir tree
openmpi-sessions-ndelader@myhost_0
orte-clean: killing any lingering procs
orte-clean: found potential rogue orterun process
(pid=2399,user=ndelader), sending SIGKILL...
orte-clean: found potential rogue orterun process
(pid=2402,user=ndelader), sending SIGKILL...
Which means that both jobs have been killed :-( Basically I would
like to perform orte-clean using executable name or PID or
whatever that identify which job I want to stop an clean. It
seems I would need to create an openmpi session per job. Does it
>> make sense ?
And
I would like to be able to do something like following command
and get following result :
% orte-clean -v myexec1
orte-clean: cleaning session dir tree
openmpi-sessions-ndelader@myhost_0
orte-clean: killing any lingering procs
orte-clean: found potential rogue orterun process
(pid=2399,user=ndelader), sending SIGKILL...
Does it make sense ? Is there a way to perform this kind of
selection in cleaning process ?
>>>
>>> How many jobs are you starting on how many nodes at one time? This
>>> requirement could be a point to start to use a queuing system,
>>> where can remove job individually and also serialize your
>>> workflow. In fact: we use GridEngine also local on workstations
>>> for this purpose.
>>>
>>> -- Reuti
>>> ___
>>> users mailing list
>>> us...@open-mpi.org
>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>>
>> __
Re: [OMPI users] Java binding requirements
Thanks for you comments. >> If so, my question is if I need NOT to install JDK to the all nodes. In >> other words is it possible to have a machine used as a worker without JDK >> installed? >> > > You do not need JDK installed on worker nodes - it only has to be on the node > where you compile your code. However, we launch a JVM for each process, so > you must at least have the JVM installed on each worker. This is typically > included in a base Linux installation (just look for the "java" command, > usually in /usr/bin), so you usually don't have to do anything special (as > opposed to installing the JDK, which doesn't usually come in the base install) Ok, but I meant to say about JVM, because my requirement is to leverage such nodes as have no JVM supported, for example, Gentoo Linux/SPARC64 as workers. I thought that the Java binding implementation wraps Open MPI only on the rank zero side. This is because the FAQ says: > 8. Do the Java bindings impact performance of my non-Java application? > The Java bindings in Open MPI are completely transparent to all other Open > MPI users and have zero performance impact on the rest of the code/bindings. But I realize that this perhaps mentions about the Open MPI applications that use a Java-enabled Open MPI build. Meantime, the next FAQ is specifying the possibility of performance penalties for Java applications that use Open MPI. Regards, --yoshiki
