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

Re: [mpich-discuss] mpich-3.0.2 and Windows
by Peter Soukalopoulos 15 Feb '13

15 Feb '13

Also interested in the Windows build. +1 from me. On Saturday, 16 February 2013, Luiz Carlos da Costa Junior wrote: > Hello all and Jayesh, > > I also work with both Linux and Windows. I am currently upgrading the > Linux version but my Windows version will be outdated. > > It is completely understandable/acceptable the limitation you have and > your development priorities. I just wanted to let you know that I would > like to add a "+1" request on the upgrade of the distribution of Windows > version. > > Only few people use the Windows version or are there more people that > might be also interested on this upgrade? > > Maybe, depending on the the number of requests, this upgrade can become > more important. > It's worth a shot. > > Regards, > > > On 15 February 2013 16:02, Jayesh Krishna <jayesh(a)mcs.anl.gov<javascript:_e({}, 'cvml', 'jayesh(a)mcs.anl.gov');> > > wrote: > >> Hi, >> Due to limited developer time available/devoted to MPICH2 >> support/development on Windows the build scripts are out-of-date. We >> currently don't have a time line on when (if) these scripts will get >> updated. Sorry for the inconvenience. >> >> Regards, >> Jayesh >> >> ----- Original Message ----- >> From: "Andrey V. Malyshev" <amal(a)icm.krasn.ru <javascript:_e({}, 'cvml', >> 'amal(a)icm.krasn.ru');>> >> To: discuss(a)mpich.org <javascript:_e({}, 'cvml', 'discuss(a)mpich.org');> >> Sent: Friday, February 15, 2013 7:51:55 AM >> Subject: [mpich-discuss] mpich-3.0.2 and Windows >> >> Hello! >> >> Is it possible to build actual release (3.0.2) on Windows? Unfortunately >> current scripts seems to be unusable. >> Or maybe Windows compatibility has broken intentionally? >> I have tryed to build and a lot of errors occurs. >> >> -- >> With best regards, Andrey V. Malyshev. >> E-mail: amal(a)krasn.ru <javascript:_e({}, 'cvml', 'amal(a)krasn.ru');> >> >> _______________________________________________ >> discuss mailing list discuss(a)mpich.org <javascript:_e({}, 'cvml', >> 'discuss(a)mpich.org');> >> To manage subscription options or unsubscribe: >> https://lists.mpich.org/mailman/listinfo/discuss >> _______________________________________________ >> discuss mailing list discuss(a)mpich.org <javascript:_e({}, 'cvml', >> 'discuss(a)mpich.org');> >> To manage subscription options or unsubscribe: >> https://lists.mpich.org/mailman/listinfo/discuss >> > > -- *Regards,* *Peter* *Peter** **Soukalopoulos* *Development Team Leader | **GreenButton *| www.greenbutton.net Level 13, Simpl House, Mercer Street, Wellington, New Zealand Mobile: +64 22 632 5023| peter.soukalopoulos(a)greenbutton.net | HQ: +644 499 0424 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.

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Re: [mpich-discuss] mpich-3.0.2 and Windows
by Luiz Carlos da Costa Junior 15 Feb '13

15 Feb '13

Hello all and Jayesh, I also work with both Linux and Windows. I am currently upgrading the Linux version but my Windows version will be outdated. It is completely understandable/acceptable the limitation you have and your development priorities. I just wanted to let you know that I would like to add a "+1" request on the upgrade of the distribution of Windows version. Only few people use the Windows version or are there more people that might be also interested on this upgrade? Maybe, depending on the the number of requests, this upgrade can become more important. It's worth a shot. Regards, On 15 February 2013 16:02, Jayesh Krishna <jayesh(a)mcs.anl.gov> wrote: > Hi, > Due to limited developer time available/devoted to MPICH2 > support/development on Windows the build scripts are out-of-date. We > currently don't have a time line on when (if) these scripts will get > updated. Sorry for the inconvenience. > > Regards, > Jayesh > > ----- Original Message ----- > From: "Andrey V. Malyshev" <amal(a)icm.krasn.ru> > To: discuss(a)mpich.org > Sent: Friday, February 15, 2013 7:51:55 AM > Subject: [mpich-discuss] mpich-3.0.2 and Windows > > Hello! > > Is it possible to build actual release (3.0.2) on Windows? Unfortunately > current scripts seems to be unusable. > Or maybe Windows compatibility has broken intentionally? > I have tryed to build and a lot of errors occurs. > > -- > With best regards, Andrey V. Malyshev. > E-mail: amal(a)krasn.ru > > _______________________________________________ > 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 >

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Re: [mpich-discuss] mpich-3.0.2 and Windows
by Jayesh Krishna 15 Feb '13

15 Feb '13

Hi, Due to limited developer time available/devoted to MPICH2 support/development on Windows the build scripts are out-of-date. We currently don't have a time line on when (if) these scripts will get updated. Sorry for the inconvenience. Regards, Jayesh ----- Original Message ----- From: "Andrey V. Malyshev" <amal(a)icm.krasn.ru> To: discuss(a)mpich.org Sent: Friday, February 15, 2013 7:51:55 AM Subject: [mpich-discuss] mpich-3.0.2 and Windows Hello! Is it possible to build actual release (3.0.2) on Windows? Unfortunately current scripts seems to be unusable. Or maybe Windows compatibility has broken intentionally? I have tryed to build and a lot of errors occurs. -- With best regards, Andrey V. Malyshev. E-mail: amal(a)krasn.ru _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Re: [mpich-discuss] Amazon ec2 Windows machine
by Jayesh Krishna 15 Feb '13

15 Feb '13

Hi, Good to know MPICH is working for you. Are the hostnames of the two ec2 instances the same? If you try to use ssm/shm with 1.4.1p1 mpiexec should abort with an error message. (PS: MPICH_NO_LOCAL=1 forces the communication in nemesis to go through tcp sockets) Regards, Jayesh ----- Original Message ----- From: "Nicholas Sgro" <nsgro060(a)gmail.com> To: "Jayesh Krishna" <jayesh(a)mcs.anl.gov> Cc: discuss(a)mpich.org Sent: Thursday, February 14, 2013 2:34:21 PM Subject: Re: [mpich-discuss] Amazon ec2 Windows machine Hi, Setting MPICH_NO_LOCAL 1 and using nemesis seems to have solved the problem. If it interests you, I tried the sock channel, and that still does not work. As far as I am concerned, there is no longer any problems. I am fairly certain that I am using version 1.4.1p1 (according to wmpiconfig), so I am not sure why I can choose shm and ssm channels (they are options in wmpiexec, and I don't get an error from command line). Thanks for your help, Nicholas On Mon, Feb 11, 2013 at 12:12 PM, Jayesh Krishna < jayesh(a)mcs.anl.gov > wrote: 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

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Re: [mpich-discuss] update online docs for MPI-3?
by Jeff Hammond 15 Feb '13

15 Feb '13

Pavan updated them for MPI-2 in 2011 (http://lists.mcs.anl.gov/pipermail/mpich-discuss/2011-September/010894.html) so you guys are doing a lot better than once every five years :-) Jeff On Fri, Feb 15, 2013 at 8:25 AM, Dave Goodell <goodell(a)mcs.anl.gov> wrote: > Hi Jeff, > > I'm not 100% sure where these files actually live on the MCS filesystem. I'll take a TODO to look for them and get them updated. Eventually these should be updated in an automated fashion, rather than once every 5 years or so :) > > -Dave > > On Feb 14, 2013, at 9:59 PM CST, Jeff Hammond wrote: > >> For example, http://www.mcs.anl.gov/research/projects/mpi/www/www3/MPI_Group_incl.html >> reflects the MPI-2 syntax, rather than that of MPI-3. >> >> Can the online docs be refreshed for MPI-3? I really like to have the >> most accurate info at hand via Google. >> >> Thanks, >> >> Jeff >> >> -- >> Jeff Hammond >> Argonne Leadership Computing Facility >> University of Chicago Computation Institute >> jhammond(a)alcf.anl.gov / (630) 252-5381 >> http://www.linkedin.com/in/jeffhammond >> https://wiki.alcf.anl.gov/parts/index.php/User:Jhammond >> _______________________________________________ >> 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 -- Jeff Hammond Argonne Leadership Computing Facility University of Chicago Computation Institute jhammond(a)alcf.anl.gov / (630) 252-5381 http://www.linkedin.com/in/jeffhammond https://wiki.alcf.anl.gov/parts/index.php/User:Jhammond

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Re: [mpich-discuss] update online docs for MPI-3?
by Dave Goodell 15 Feb '13

15 Feb '13

Hi Jeff, I'm not 100% sure where these files actually live on the MCS filesystem. I'll take a TODO to look for them and get them updated. Eventually these should be updated in an automated fashion, rather than once every 5 years or so :) -Dave On Feb 14, 2013, at 9:59 PM CST, Jeff Hammond wrote: > For example, http://www.mcs.anl.gov/research/projects/mpi/www/www3/MPI_Group_incl.html > reflects the MPI-2 syntax, rather than that of MPI-3. > > Can the online docs be refreshed for MPI-3? I really like to have the > most accurate info at hand via Google. > > Thanks, > > Jeff > > -- > Jeff Hammond > Argonne Leadership Computing Facility > University of Chicago Computation Institute > jhammond(a)alcf.anl.gov / (630) 252-5381 > http://www.linkedin.com/in/jeffhammond > https://wiki.alcf.anl.gov/parts/index.php/User:Jhammond > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss

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mpich-3.0.2 and Windows
by Andrey V. Malyshev 15 Feb '13

15 Feb '13

Hello! Is it possible to build actual release (3.0.2) on Windows? Unfortunately current scripts seems to be unusable. Or maybe Windows compatibility has broken intentionally? I have tryed to build and a lot of errors occurs. -- With best regards, Andrey V. Malyshev. E-mail: amal(a)krasn.ru

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update online docs for MPI-3?
by Jeff Hammond 14 Feb '13

14 Feb '13

For example, http://www.mcs.anl.gov/research/projects/mpi/www/www3/MPI_Group_incl.html reflects the MPI-2 syntax, rather than that of MPI-3. Can the online docs be refreshed for MPI-3? I really like to have the most accurate info at hand via Google. Thanks, Jeff -- Jeff Hammond Argonne Leadership Computing Facility University of Chicago Computation Institute jhammond(a)alcf.anl.gov / (630) 252-5381 http://www.linkedin.com/in/jeffhammond https://wiki.alcf.anl.gov/parts/index.php/User:Jhammond

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Re: [mpich-discuss] Amazon ec2 Windows machine
by Nicholas Sgro 14 Feb '13

14 Feb '13

Hi, Setting MPICH_NO_LOCAL 1 and using nemesis seems to have solved the problem. If it interests you, I tried the sock channel, and that still does not work. As far as I am concerned, there is no longer any problems. I am fairly certain that I am using version 1.4.1p1 (according to wmpiconfig), so I am not sure why I can choose shm and ssm channels (they are options in wmpiexec, and I don't get an error from command line). Thanks for your help, Nicholas On Mon, Feb 11, 2013 at 12:12 PM, Jayesh Krishna <jayesh(a)mcs.anl.gov> wrote: > 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 >

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Re: [mpich-discuss] Inside Collective calls
by Dave Goodell 13 Feb '13

13 Feb '13

On Feb 13, 2013, at 10:59 AM CST, m srini wrote: > 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. Most of those same patterns/algorithms are still in use. The most accurate way to determine what is used is to examine the source, particularly the sources in the "src/mpi/coll" directory: http://git.mpich.org/mpich.git/tree/HEAD:/src/mpi/coll -Dave

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