February 2013 - discuss - mailman3.cels.anl.gov

Inside Collective calls
by m srini 13 Feb '13

13 Feb '13

Hello sir, I have a small doubt regarding the patterns that the collective calls use. Do they still use the patterns mentioned in the paper "OPTIMIZING MPI COLLECTIVE CALLS" by Rajeev Thakur ? If not please help me in understanding the collective call patterns. Thanks a lot. With warm regards, M.Srinivas

1 0

Re: [mpich-discuss] Windows installer for MPICH v3.0.2
by Jayesh Krishna 12 Feb '13

12 Feb '13

Hi, Due to limited developer bandwidth we haven't been able to keep the Windows source/builds up-to-date . Unfortunately we don't have a time frame when (if) we will get to it. Regards, Jayesh ----- Original Message ----- From: "Peter Soukalopoulos" <peter(a)greenbutton.com> To: mpich-discuss(a)mcs.anl.gov Sent: Monday, February 11, 2013 6:14:34 PM Subject: [mpich-discuss] Windows installer for MPICH v3.0.2 Hi, I’m looking for an updated Windows installer. I tried building from sources but it’s based on VS 2005 – now running VS 2012! Had some problem trying to upgrade. Many thanks. Regards, Peter Peter Soukalopoulos Development Team Leader | GreenButton Limited | www.greenbutton.com Level 13, Simpl House, 40 Mercer Street, Wellington, New Zealand Mobile: +64 22 632 5023 | peter.soukalopoulos(a)greenbutton.com | Skype : psoukal | HQ : +644 499 0424 Description: GreenButton_words_smallcid:[email protected] For best support, please respond to help(a)greenbutton.com and retain the ticket number in the subject line. This message contains confidential information, intended only for the person(s) named above, which may also be privileged. Any use, distribution, copying or disclosure by any other person is strictly prohibited. In such case, you should delete this message and kindly notify the sender via reply e-mail. Please advise immediately if you or your employer does not consent to Internet e-mail for messages of this kind. _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

1 0

Windows installer for MPICH v3.0.2
by Peter Soukalopoulos 11 Feb '13

11 Feb '13

Hi, I'm looking for an updated Windows installer. I tried building from sources but it's based on VS 2005 - now running VS 2012! Had some problem trying to upgrade. Many thanks. Regards, Peter Peter Soukalopoulos Development Team Leader | GreenButton Limited | www.greenbutton.com <http://www.greenbutton.com/> Level 13, Simpl House, 40 Mercer Street, Wellington, New Zealand Mobile: +64 22 632 5023| peter.soukalopoulos(a)greenbutton.com | Skype: psoukal | HQ: +644 499 0424 Description: GreenButton_words_small cid:[email protected] For best support, please respond to help(a)greenbutton.com and retain the ticket number in the subject line. This message contains confidential information, intended only for the person(s) named above, which may also be privileged. Any use, distribution, copying or disclosure by any other person is strictly prohibited. In such case, you should delete this message and kindly notify the sender via reply e-mail. Please advise immediately if you or your employer does not consent to Internet e-mail for messages of this kind.

1 0

Re: [mpich-discuss] running parallel on windows
by Jayesh Krishna 11 Feb '13

11 Feb '13

Hi, Can you run the sample MPI program, cpi.exe (c:\Program Files\MPICH2\examples\cpi.exe)? Regards, Jayesh ----- Original Message ----- From: "farrokh yousefi" <farrokhyousefi62(a)gmail.com> To: discuss(a)mpich.org Sent: Saturday, February 9, 2013 7:41:07 AM Subject: Re: [mpich-discuss] running parallel on windows Dear all, I want to run an example on windows in parallel, after installation MPICH2 and Putting smpd.exe & mpiexec.exe in the directory, when i write : mpiexec -np 1 -localonly lmp_win_mpi -in in.melt everything is working fine! (e.g: after passphrase for smpd, it run on single processor) but when i write: mpiexec -np 2 -localonly lmp_win_mpi -in in.melt does not work.(e.g after passphrase, does not run and stops! and does not issue any error). Please help me. Thank you Yasti _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

1 0

Re: [mpich-discuss] Amazon ec2 Windows machine
by Jayesh Krishna 11 Feb '13

11 Feb '13

Hi, The latest version of MPICH2 on Windows (1.4.1p1) do not have support for shm and ssm channels. Are you sure you are using the latest version of MPICH2 on your machines? Please use the "-channel" option to select the channels ("nemesis"/"sock"). Can you try running the job by setting the environment variable "MPICH_NO_LOCAL" to 1 (mpiexec -n 2 -env MPICH_NO_LOCAL 1 c:\Progra~1\MPICH2\examples\cpi.exe)? This option should force all communication to go via tcp sockets. Regards, Jayesh ----- Original Message ----- From: "Nicholas Sgro" <nsgro060(a)gmail.com> To: "Rayson Ho" <raysonlogin(a)gmail.com> Cc: discuss(a)mpich.org Sent: Sunday, February 10, 2013 3:46:27 PM Subject: Re: [mpich-discuss] Amazon ec2 Windows machine Both instances are part of the same security group, and I made sure all inbound traffic was allowed. StarCluster looks very useful. Can you recommend something similar to StarCluster but for windows instances? The software I am using is only available for windows. thanks, Nicholas On Sun, Feb 10, 2013 at 1:57 PM, Rayson Ho < raysonlogin(a)gmail.com > wrote: How did you configure the EC2 security groups? By default, EC2 instances have their inbound traffic blocked, and you will need to configure security group rules to enable inbound traffic. http://docs.aws.amazon.com/AWSEC2/latest/UserGuide/using-network-security.h… Also, any reason you are manually creating EC2 HPC clusters instead of using a toolkit?? We are a fan of MIT's StarCluster -- with it we can start up and shut down clusters very quickly (usually a few minutes). It is Linux based, with MPICH (and/or Open MPI), Open Grid Scheduler / Grid Engine, and many tools needed for doing HPC in EC2: http://star.mit.edu/cluster/ And we built a 10,000-node cluster in EC2 based on StarCluster late last year, during SC12: http://blogs.scalablelogic.com/2012/11/running-10000-node-grid-engine-clust… Rayson ================================================== Open Grid Scheduler - The Official Open Source Grid Engine http://gridscheduler.sourceforge.net/ On Fri, Feb 8, 2013 at 5:02 PM, Nicholas Sgro < nsgro060(a)gmail.com > wrote: > Hi, > This is the command I'm using: > > mpiexec.exe -machinefile machines.txt -env MPICH2_CHANNEL sock -n 2 cpi.exe > > I have tried using both machine file and hosts in the command line, but I > get the same results. The program runs on a single instance with any number > of processors. I tried running mpiexec on one instance and using the other > as a single host and that also works. > > -Nicholas > > > On Fri, Feb 8, 2013 at 12:04 PM, Jayesh Krishna < jayesh(a)mcs.anl.gov > wrote: >> >> Hi, >> How are you running your job (mpiexec command)? Did you try using a >> machine file to specify the hostnames when running the job? >> Does the program (cpi) execute correctly on a single ec2 instance? >> >> Regards, >> Jayesh >> >> ----- Original Message ----- >> From: "Nicholas Sgro" < nsgro060(a)gmail.com > >> To: "Jayesh Krishna" < jayesh(a)mcs.anl.gov > >> Sent: Thursday, February 7, 2013 9:57:55 PM >> Subject: Re: [mpich-discuss] Amazon ec2 Windows machine >> >> I'm using version 1.4.1p1. I tried the sock channel. It doesn't seem to >> work either. With sock, I get to the point where I enter the number of >> intervals, but then it does nothing. >> >> Do you know any reason it wouldn't work with ec2 instances? >> >> >> >> On Thu, Feb 7, 2013 at 4:29 PM, Jayesh Krishna < jayesh(a)mcs.anl.gov > >> wrote: >> >> >> Hi, >> Which version of MPICH2 are you using? Did you try the "sock" channel (See >> if it works)? >> >> (PS: We haven't tested MPICH2 on Windows with ec2 instances.) >> Regards, >> Jayesh >> >> >> ----- Original Message ----- >> From: "Nicholas Sgro" < nsgro060(a)gmail.com > >> To: discuss(a)mpich.org >> Sent: Thursday, February 7, 2013 11:29:57 AM >> Subject: [mpich-discuss] Amazon ec2 Windows machine >> >> >> Hi all, >> >> I am trying to run the example cpi.exe across 2 amazon ec2 instances >> running windows. I have different problems depending on the channel I >> choose. If I try nemesis, I get the following error: >> >> Fatal error in MPI_Init: Other MPI error, error stack: >> MPIR_Init_thread(392).................: >> MPID_Init(139)........................: channel initialization failed >> MPIDI_CH3_Init(38)....................: >> MPID_nem_init(196)....................: >> MPIDI_CH3I_Seg_commit(366)............: >> MPIU_SHMW_Hnd_deserialize(324)........: >> MPIU_SHMW_Seg_open(863)...............: >> MPIU_SHMW_Seg_create_attach_templ(763): unable to allocate shared memory - >> OpenFileMapping The system cannot find the file specified. >> >> If I try to use shm, cpi.exe uses 100% of the processors on both machines, >> but makes no progress and I have to cancel the job. >> >> I am attaching logs from smpd from both machines from the runs with >> nemesis and shm. >> >> I don't have any experience with mpich, so I have no idea what the problem >> is. Any guidance would be appreciated. >> >> Thanks >> >> >> _______________________________________________ >> discuss mailing list discuss(a)mpich.org >> To manage subscription options or unsubscribe: >> https://lists.mpich.org/mailman/listinfo/discuss >> > > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

1 0

Re: [mpich-discuss] Amazon ec2 Windows machine
by Nicholas Sgro 10 Feb '13

10 Feb '13

Both instances are part of the same security group, and I made sure all inbound traffic was allowed. StarCluster looks very useful. Can you recommend something similar to StarCluster but for windows instances? The software I am using is only available for windows. thanks, Nicholas On Sun, Feb 10, 2013 at 1:57 PM, Rayson Ho <raysonlogin(a)gmail.com> wrote: > How did you configure the EC2 security groups? By default, EC2 > instances have their inbound traffic blocked, and you will need to > configure security group rules to enable inbound traffic. > > > http://docs.aws.amazon.com/AWSEC2/latest/UserGuide/using-network-security.h… > > Also, any reason you are manually creating EC2 HPC clusters instead of > using a toolkit?? We are a fan of MIT's StarCluster -- with it we can > start up and shut down clusters very quickly (usually a few minutes). > It is Linux based, with MPICH (and/or Open MPI), Open Grid Scheduler / > Grid Engine, and many tools needed for doing HPC in EC2: > > http://star.mit.edu/cluster/ > > And we built a 10,000-node cluster in EC2 based on StarCluster late > last year, during SC12: > > > http://blogs.scalablelogic.com/2012/11/running-10000-node-grid-engine-clust… > > Rayson > > ================================================== > Open Grid Scheduler - The Official Open Source Grid Engine > http://gridscheduler.sourceforge.net/ > > > On Fri, Feb 8, 2013 at 5:02 PM, Nicholas Sgro <nsgro060(a)gmail.com> wrote: > > Hi, > > This is the command I'm using: > > > > mpiexec.exe -machinefile machines.txt -env MPICH2_CHANNEL sock -n 2 > cpi.exe > > > > I have tried using both machine file and hosts in the command line, but I > > get the same results. The program runs on a single instance with any > number > > of processors. I tried running mpiexec on one instance and using the > other > > as a single host and that also works. > > > > -Nicholas > > > > > > On Fri, Feb 8, 2013 at 12:04 PM, Jayesh Krishna <jayesh(a)mcs.anl.gov> > wrote: > >> > >> Hi, > >> How are you running your job (mpiexec command)? Did you try using a > >> machine file to specify the hostnames when running the job? > >> Does the program (cpi) execute correctly on a single ec2 instance? > >> > >> Regards, > >> Jayesh > >> > >> ----- Original Message ----- > >> From: "Nicholas Sgro" <nsgro060(a)gmail.com> > >> To: "Jayesh Krishna" <jayesh(a)mcs.anl.gov> > >> Sent: Thursday, February 7, 2013 9:57:55 PM > >> Subject: Re: [mpich-discuss] Amazon ec2 Windows machine > >> > >> I'm using version 1.4.1p1. I tried the sock channel. It doesn't seem to > >> work either. With sock, I get to the point where I enter the number of > >> intervals, but then it does nothing. > >> > >> Do you know any reason it wouldn't work with ec2 instances? > >> > >> > >> > >> On Thu, Feb 7, 2013 at 4:29 PM, Jayesh Krishna < jayesh(a)mcs.anl.gov > > >> wrote: > >> > >> > >> Hi, > >> Which version of MPICH2 are you using? Did you try the "sock" channel > (See > >> if it works)? > >> > >> (PS: We haven't tested MPICH2 on Windows with ec2 instances.) > >> Regards, > >> Jayesh > >> > >> > >> ----- Original Message ----- > >> From: "Nicholas Sgro" < nsgro060(a)gmail.com > > >> To: discuss(a)mpich.org > >> Sent: Thursday, February 7, 2013 11:29:57 AM > >> Subject: [mpich-discuss] Amazon ec2 Windows machine > >> > >> > >> Hi all, > >> > >> I am trying to run the example cpi.exe across 2 amazon ec2 instances > >> running windows. I have different problems depending on the channel I > >> choose. If I try nemesis, I get the following error: > >> > >> Fatal error in MPI_Init: Other MPI error, error stack: > >> MPIR_Init_thread(392).................: > >> MPID_Init(139)........................: channel initialization failed > >> MPIDI_CH3_Init(38)....................: > >> MPID_nem_init(196)....................: > >> MPIDI_CH3I_Seg_commit(366)............: > >> MPIU_SHMW_Hnd_deserialize(324)........: > >> MPIU_SHMW_Seg_open(863)...............: > >> MPIU_SHMW_Seg_create_attach_templ(763): unable to allocate shared > memory - > >> OpenFileMapping The system cannot find the file specified. > >> > >> If I try to use shm, cpi.exe uses 100% of the processors on both > machines, > >> but makes no progress and I have to cancel the job. > >> > >> I am attaching logs from smpd from both machines from the runs with > >> nemesis and shm. > >> > >> I don't have any experience with mpich, so I have no idea what the > problem > >> is. Any guidance would be appreciated. > >> > >> Thanks > >> > >> > >> _______________________________________________ > >> discuss mailing list discuss(a)mpich.org > >> To manage subscription options or unsubscribe: > >> https://lists.mpich.org/mailman/listinfo/discuss > >> > > > > > > _______________________________________________ > > discuss mailing list discuss(a)mpich.org > > To manage subscription options or unsubscribe: > > https://lists.mpich.org/mailman/listinfo/discuss >

1 0

Re: [mpich-discuss] Amazon ec2 Windows machine
by Rayson Ho 10 Feb '13

10 Feb '13

How did you configure the EC2 security groups? By default, EC2 instances have their inbound traffic blocked, and you will need to configure security group rules to enable inbound traffic. http://docs.aws.amazon.com/AWSEC2/latest/UserGuide/using-network-security.h… Also, any reason you are manually creating EC2 HPC clusters instead of using a toolkit?? We are a fan of MIT's StarCluster -- with it we can start up and shut down clusters very quickly (usually a few minutes). It is Linux based, with MPICH (and/or Open MPI), Open Grid Scheduler / Grid Engine, and many tools needed for doing HPC in EC2: http://star.mit.edu/cluster/ And we built a 10,000-node cluster in EC2 based on StarCluster late last year, during SC12: http://blogs.scalablelogic.com/2012/11/running-10000-node-grid-engine-clust… Rayson ================================================== Open Grid Scheduler - The Official Open Source Grid Engine http://gridscheduler.sourceforge.net/ On Fri, Feb 8, 2013 at 5:02 PM, Nicholas Sgro <nsgro060(a)gmail.com> wrote: > Hi, > This is the command I'm using: > > mpiexec.exe -machinefile machines.txt -env MPICH2_CHANNEL sock -n 2 cpi.exe > > I have tried using both machine file and hosts in the command line, but I > get the same results. The program runs on a single instance with any number > of processors. I tried running mpiexec on one instance and using the other > as a single host and that also works. > > -Nicholas > > > On Fri, Feb 8, 2013 at 12:04 PM, Jayesh Krishna <jayesh(a)mcs.anl.gov> wrote: >> >> Hi, >> How are you running your job (mpiexec command)? Did you try using a >> machine file to specify the hostnames when running the job? >> Does the program (cpi) execute correctly on a single ec2 instance? >> >> Regards, >> Jayesh >> >> ----- Original Message ----- >> From: "Nicholas Sgro" <nsgro060(a)gmail.com> >> To: "Jayesh Krishna" <jayesh(a)mcs.anl.gov> >> Sent: Thursday, February 7, 2013 9:57:55 PM >> Subject: Re: [mpich-discuss] Amazon ec2 Windows machine >> >> I'm using version 1.4.1p1. I tried the sock channel. It doesn't seem to >> work either. With sock, I get to the point where I enter the number of >> intervals, but then it does nothing. >> >> Do you know any reason it wouldn't work with ec2 instances? >> >> >> >> On Thu, Feb 7, 2013 at 4:29 PM, Jayesh Krishna < jayesh(a)mcs.anl.gov > >> wrote: >> >> >> Hi, >> Which version of MPICH2 are you using? Did you try the "sock" channel (See >> if it works)? >> >> (PS: We haven't tested MPICH2 on Windows with ec2 instances.) >> Regards, >> Jayesh >> >> >> ----- Original Message ----- >> From: "Nicholas Sgro" < nsgro060(a)gmail.com > >> To: discuss(a)mpich.org >> Sent: Thursday, February 7, 2013 11:29:57 AM >> Subject: [mpich-discuss] Amazon ec2 Windows machine >> >> >> Hi all, >> >> I am trying to run the example cpi.exe across 2 amazon ec2 instances >> running windows. I have different problems depending on the channel I >> choose. If I try nemesis, I get the following error: >> >> Fatal error in MPI_Init: Other MPI error, error stack: >> MPIR_Init_thread(392).................: >> MPID_Init(139)........................: channel initialization failed >> MPIDI_CH3_Init(38)....................: >> MPID_nem_init(196)....................: >> MPIDI_CH3I_Seg_commit(366)............: >> MPIU_SHMW_Hnd_deserialize(324)........: >> MPIU_SHMW_Seg_open(863)...............: >> MPIU_SHMW_Seg_create_attach_templ(763): unable to allocate shared memory - >> OpenFileMapping The system cannot find the file specified. >> >> If I try to use shm, cpi.exe uses 100% of the processors on both machines, >> but makes no progress and I have to cancel the job. >> >> I am attaching logs from smpd from both machines from the runs with >> nemesis and shm. >> >> I don't have any experience with mpich, so I have no idea what the problem >> is. Any guidance would be appreciated. >> >> Thanks >> >> >> _______________________________________________ >> discuss mailing list discuss(a)mpich.org >> To manage subscription options or unsubscribe: >> https://lists.mpich.org/mailman/listinfo/discuss >> > > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss

1 0

Re: [mpich-discuss] MPI RMA
by Jim Dinan 09 Feb '13

09 Feb '13

Hi Jed, The MPI standard doesn't mandate a particular behavior in case of an error, so doing what the user asked for is also allowed. :) In seriousness, I completely agree on the importance of error checking. The coverage in RMA has improved significantly through the MPI-3 development effort, and we are continuing to work on it. ~Jim. On 2/8/13 1:16 PM, Jed Brown wrote: > > On Fri, Feb 8, 2013 at 1:08 PM, Jim Dinan <dinan(a)mcs.anl.gov > <mailto:[email protected]>> wrote: > > However, it will work fine in MPICH. In MPICH 3.0, I redesigned the > synchronization error detection; as of 3.0, this is the only invalid > RMA synchronization where we don't flag an error. This is not so > much because we choose to support this as an extension to RMA, but > because the flush state needs to change collectively, making this > difficult (not O(1)) to detect. > > > If this is really the only instance, it may not be worth it, but in > general, it's helpful to have a run-time (or even compile-time, if > necessary) option that does the strictest checking you're willing to > implement, even when it implies a performance hit. Certainly useful for > people trying to determine whether they have interpreted the standard > correctly, or when given someone else's code that is failing mysteriously. > > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss >

1 0

Re: [mpich-discuss] running parallel on windows
by farrokh yousefi 09 Feb '13

09 Feb '13

Dear all, I want to run an example on windows in parallel, after installation MPICH2 and Putting smpd.exe & mpiexec.exe in the directory, when i write : mpiexec -np 1 -localonly lmp_win_mpi -in in.melt everything is working fine! (e.g: after passphrase for smpd, it run on single processor) but when i write: mpiexec -np 2 -localonly lmp_win_mpi -in in.melt does not work.(e.g after passphrase, does not run and stops! and does not issue any error). Please help me. Thank you Yasti

1 0

running parallel on windows
by farrokh yousefi 09 Feb '13

09 Feb '13

Dear all, I want to run an example on windows in parallel, after installation MPICH2 and Putting smpd.exe & mpiexec.exe in the directory, when i write : mpiexec -np 1 -localonly lmp_win_mpi -in in.melt everything is working fine! (e.g: after passphrase for smpd, it run on single processor) but when i write: mpiexec -np 2 -localonly lmp_win_mpi -in in.melt does not work.(e.g after passphrase, does not run and stops! and does not issue any error). Please help me. Thank you Yasti

1 0