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Re: [mpich-discuss] Weird performance of locally concurrent MPI_Put
by Si, Min 21 Dec '18

21 Dec '18

Hi Kun, Can you please try MPI_Win_allocate instead of MPI_Win_create in your program ? Single memory copy based MPI_Put is enabled only for MPI_Win_allocate in current MPICH. Best regards, Min On 2018/12/21 10:15, Kun Feng via discuss wrote: Hi all, I'm working on a project in which one half of the processes need to send data to the other half in each node. I'm using passive target mode of one-sided communication in which the receivers expose memory using MPI_Win_create, wait on MPI_Win_free and the senders send the data using MPI_Put. The code works. However, I get weird performance using this concurrent MPI_Put communication. The peak aggregate bandwidth is only around 5GB/s. It does not make sense as an aggregate performance in one single node. I thought the node-local communication is implemented as local memcpy. But concurrent memcpy on the same testbed has 4x to 5x higher aggregate bandwidth. Even concurrent memcpy using Linux shared memory across processes is 3x faster than my code. I'm using CH3 in MPICH 3.2.1. CH4 in MPICH 3.3 is even 2x slower. Does the performance make sense? Does MPICH has some queue for all one-sided communication in one node? Or do I understand it incorrectly? Thanks Kun _______________________________________________ discuss mailing list discuss(a)mpich.org<mailto:[email protected]> To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Weird performance of locally concurrent MPI_Put
by Kun Feng 21 Dec '18

21 Dec '18

Hi all, I'm working on a project in which one half of the processes need to send data to the other half in each node. I'm using passive target mode of one-sided communication in which the receivers expose memory using MPI_Win_create, wait on MPI_Win_free and the senders send the data using MPI_Put. The code works. However, I get weird performance using this concurrent MPI_Put communication. The peak aggregate bandwidth is only around 5GB/s. It does not make sense as an aggregate performance in one single node. I thought the node-local communication is implemented as local memcpy. But concurrent memcpy on the same testbed has 4x to 5x higher aggregate bandwidth. Even concurrent memcpy using Linux shared memory across processes is 3x faster than my code. I'm using CH3 in MPICH 3.2.1. CH4 in MPICH 3.3 is even 2x slower. Does the performance make sense? Does MPICH has some queue for all one-sided communication in one node? Or do I understand it incorrectly? Thanks Kun

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Re: [mpich-discuss] how to dynamically schedule process in mpich
by Shuwei Zhao 17 Dec '18

17 Dec '18

Hi, Zhou, Sorry for the late reply, I was busy with some customer requests. Yes my system is UGE similar to SGE. Your explanation makes a lot senses. I haven't had a chance to verify it. I'll try it later. Thank you a lot for your explanations. I have great learning experiences in the discussion forum. Wish you and your team member have a nice holiday! Thanks, Shuwei On Thu, Nov 29, 2018 at 5:17 PM Zhou, Hui <zhouh(a)anl.gov> wrote: > What is your system? PBS? You have to prescribe a pool of nodes with qsub > and run mpiexec -n 1 (for example). Then when you launch additional mpi > process dynamically, hydra will spawn new processes within the prescribed > pool. If your original pool is a single host, then all new dynamic process > will be on that single host. If you describe multiple hosts, I believe > hydra will do round-robin style allocation, i.e. the next processes will go > to host 2, host 3, …., host N, host 1 (circle back). > > This is my current understanding. Let me know whether you can confirm. > > — > Hui Zhou > > > > On Nov 29, 2018, at 4:41 PM, Shuwei Zhao <shuweizhao1991(a)gmail.com> wrote: > > Hi Hui > > I cannot run mpiexec directly on my hosts because both rsh and ssh > connections are disabled. I have to use qsub -P bnormal -pe dp 4 mpiexec > ./my_exe to run my binary on remote hosts. > > Thanks > Shuwei > >> >> >

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mpiexec tries to connect to one of my Ethernet connections
by Payman Shamlu 12 Dec '18

12 Dec '18

I use OpenVPN system on my pc, and while I want to use the mpiexec it run too slowly ( e.g. takes 1min to run hello world), but when I disable the ethernet connection that corresponds to the Openvpn, mpiexec works promptly. The problem is that I cant use both my OpenVPN and mpiexec at the same time every time I have to disable it. How can I be able to stop the mpiexec to connect to the OpenVpn?

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Re: [mpich-discuss] MPI_Comm_spawn zombies have risen from the dead.
by Thomas Pak 11 Dec '18

11 Dec '18

Hi Hui, Sorry the late response. No problem! The application that I am developing is a tool that automates the parallelisation of scientific simulations as part of an advanced parameter sweeping algorithm. One of the key goals is to do this in a modular manner. I have decided to let the simulation be performed by an executable provided by the user, a so-called "simulator". This provides the most flexibility as the user can then write their simulator in any programming or scripting language. Moreover, this also implies that the user can make use of any software package or library. For regular non-MPI simulators, my application invokes the simulator with the system calls fork() and exec(). These types of simulator work perfectly fine with my application as it currently stands. However, when the simulator itself uses MPI, the fork-exec fails because an MPI application forking another MPI application is undefined and causes all kinds of troubles. Thus, I have resorted to using the native MPI_Comm_spawn function for dynamic process management for those cases. A possible counterpoint to all of this is that there is no use in running parallel instances of an MPI simulator because the simulator itself parallelised. However, this is not always the case because some simulation software packages are written using external libraries that use MPI internally, such as PETSc, despite the application itself not being parallelised. Even though this case might be somewhat niche, it is exactly the situation that I am in. In summary, my MPI application calls external executables provided by the user and runs many parallel instances of them. The external executable itself may be an MPI application, in which case MPI_Comm_spawn is necessary. In a way, the reason I need MPI_Comm_spawn to work is because MPI has become so ubiquitous in scientific computing that even non-parallelised simulators might be using MPI under the hood. I hope this helps. Best wishes, Thomas Pak On Dec 6 2018, at 4:00 pm, Zhou, Hui <zhouh(a)anl.gov> wrote: > Hi Thomas, > > Sure. While I am finding time looking into this, could you talk a bit more about your application? The dynamic MPI processes is still a new territory despite its presence for many years. One of the reasons is due to lack of exposure for such applications. > > — > Hui Zhou > > > > > On Dec 6, 2018, at 6:11 AM, Thomas Pak <thomas.pak(a)maths.ox.ac.uk (mailto:[email protected])> wrote: > > Hi Hui, > > That is exactly right, thanks so much for looking into it! Please let me know if you make any progress on this issue, as the application I am developing critically depends on MPI_Comm_spawn. > > Best wishes, > > Thomas Pak > > > > > >

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Re: [mpich-discuss] symbol lookup error
by Congiu, Giuseppe 06 Dec '18

06 Dec '18

Hi Haider, I would suggest, if you are not already doing that, to build and install mpich yourself in your home (which hopefully resides on a network file system mounted on all the machines of the cluster). Please use the latest stable tarball distribution (you can find it at: https://www.mpich.org/downloads/) In the README you can find instructions on how to configure and build the library. Don’t forget to add your installation path to the PATH environment or else you will still be running with the system installation instead of your local one. Best, Giuseppe On Dec 5, 2018, at 11:47 PM, Haider Abbas via discuss <discuss(a)mpich.org<mailto:[email protected]>> wrote: Dear Giuseppe, You are right, node 4 and node 6 are not working properly. when I am running pw.x on these node, it gives ./pw.x -i relax2.in<http://relax2.in/> >out.out & [1] 8475 mpiuser@node4:~/qe-29-11/bin$ ./pw.x: symbol lookup error: ./pw.x: undefined symbol: mpi_initialized_ I have reinstalled gfortran and mpich but still facing the same problem. Could you please further guide me how to overcome this problem. regards Haider Abbas On Wed, Dec 5, 2018 at 9:17 PM Congiu, Giuseppe via discuss <discuss(a)mpich.org<mailto:[email protected]>> wrote: Hello Haider, Are you compiling mpich and installing it in a global path accessible to all machines or you are using local installations? The missing symbol is a fortran symbol. The fact it is not there can mean mpich was not compiled with fortran support while your application is a fortran code. The fact that it works for a certain number of processes might mean some machine do have fortran support while other machines don’t. Can you provide some additional information about your cluster configuration? The MPICH version you are running and how you are configuring it? --Giuseppe On Dec 5, 2018, at 1:53 AM, Haider Abbas via discuss <discuss(a)mpich.org<mailto:[email protected]>> wrote: mpi_initialized_ _______________________________________________ discuss mailing list discuss(a)mpich.org<mailto:[email protected]> To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss _______________________________________________ discuss mailing list discuss(a)mpich.org<mailto:[email protected]> To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Re: [mpich-discuss] MPI_Comm_spawn zombies have risen from the dead.
by Zhou, Hui 06 Dec '18

06 Dec '18

Hi Thomas, Sure. While I am finding time looking into this, could you talk a bit more about your application? The dynamic MPI processes is still a new territory despite its presence for many years. One of the reasons is due to lack of exposure for such applications. — Hui Zhou On Dec 6, 2018, at 6:11 AM, Thomas Pak <thomas.pak(a)maths.ox.ac.uk<mailto:[email protected]>> wrote: Hi Hui, That is exactly right, thanks so much for looking into it! Please let me know if you make any progress on this issue, as the application I am developing critically depends on MPI_Comm_spawn. Best wishes, Thomas Pak

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Re: [mpich-discuss] MPI_Comm_spawn zombies have risen from the dead.
by Thomas Pak 06 Dec '18

06 Dec '18

Hi Hui, That is exactly right, thanks so much for looking into it! Please let me know if you make any progress on this issue, as the application I am developing critically depends on MPI_Comm_spawn. Best wishes, Thomas Pak On Dec 6 2018, at 1:57 pm, Zhou, Hui <zhouh(a)anl.gov> wrote: > > Hi Thomas, > > To summarize issue: MPICH proxy does not reap processes after its exit? > > I’ll look into the issue. From my peruse of current MPI standards, it does not really specify the behavior after MPI_Finalize. The dynamic process part of MPI support is weak, primary due to lack of application adoption. Regardless, I agree that the proxy creates the process should be responsible to reap its dead children. > > — > Hui Zhou > > > > > > > > > > On Dec 6, 2018, at 3:53 AM, Thomas Pak via discuss <discuss(a)mpich.org (mailto:[email protected])> wrote: > > Dear all, > > Does anyone have any feedback on this issue? The problem still persists in MPICH-3.3 and it seems like it is pointing to a severe flaw in how MPICH handles dynamic process creation. To reiterate, the following short program using MPICH creates zombie processes indefinitely until no more processes can be created. > > """ > > #include <stdio.h> > > #include <mpi.h> > > > > int main(int argc, char *argv[]) { > > // Initialize MPI > > MPI_Init(NULL, NULL); > > > > // Get parent > > MPI_Comm parent; > > MPI_Comm_get_parent(&parent); > > > > // If the process was not spawned > > if (parent == MPI_COMM_NULL) { > > > > puts("I was not spawned!"); > > // Spawn child process in loop > > char *cmd = argv[0]; > > char **cmd_argv = MPI_ARGV_NULL; > > int maxprocs = 1; > > MPI_Info info = MPI_INFO_NULL; > > int root = 0; > > MPI_Comm comm = MPI_COMM_SELF; > > MPI_Comm intercomm; > > int *array_of_errcodes = MPI_ERRCODES_IGNORE; > > > > for (;;) { > > MPI_Comm_spawn(cmd, cmd_argv, maxprocs, info, root, comm, > > &intercomm, array_of_errcodes); > > > > MPI_Comm_disconnect(&intercomm); > > } > > > > // If process was spawned > > } else { > > > > puts("I was spawned!"); > > MPI_Comm_disconnect(&parent); > > } > > > > // Finalize > > MPI_Finalize(); > > > > } > > """ > > > > Thanks in advance for your help. > > Best wishes, > > Thomas Pak > > > > On Oct 16 2018, at 4:57 pm, Thomas Pak <thomas.pak(a)maths.ox.ac.uk (mailto:[email protected])> wrote: > > > > > > Dear all, > > > My MPI application spawns a large number of MPI processes using MPI_Comm_spawn over its total lifetime. Unfortunately, I have experienced that this results in zombie processes of hydra_pmi_proxy accumulating over time. As a result, my MPI application will eventually crash because there are too many zombie processes and no new processes can be created. > > > This issue does not seem to be new; I have found references to similar issues in at least three different places: > > > - [mpich-discuss] MPI_Comm_Spawn causing zombies of hydra_pmi_proxy (https://lists.mpich.org/pipermail/discuss/2013-March/000599.html) (March 2013) > > > - [GitHub issue] hydra_pmi_proxy zombie MPI_comm_spawn #1677 (https://github.com/pmodels/mpich/issues/1677) (October 2016) > > > - [Google Groups] Hanging in spawn in master-slave code and hydra_pmi_proxy zombies (https://groups.google.com/forum/#!msg/mpi4py/A9mN-2UkFf8/2gnUEtArDwAJ) (December 2016) > > > In the first reference, a dirty fix was proposed by Silvan Brändli to simply reap all the zombie processes in a loop at the start of the function HYDU_create_process in src/pm/hydra/utils/launch/launch.c. However, I have found that this comes with its own set of problems and makes my MPI application unstable. > > > > > > In the GitHub issue, the problem was marked as "worksforme". However, this problem persists for me and other machines that I have tried to reproduce it on, so it clearly has not yet been resolved. > > > In the Google Groups thread, the problem was "resolved" by avoiding spawning MPI processes entirely, which is not an option in my case. > > > Pavan Balaji mentions in the 2013 mpi-discuss thread that this issue was a problem "once upon a time". It seems to have risen from the dead again. > > > I have attached a short and self-contained program written in C that reproduces the problem. The program simply spawns child processes using MPI_Comm_spawn in an infinite loop, where each child process exits after writing a message to stdout. I use MPI_Comm_disconnect to disconnect the Intercommunicator, but the same problem occurs when using MPI_Comm_free instead. > > > I have also attached the logfiles generated while building MPICH, as described in the README, except for the file mpich-3.2.1/src/pm/hydra/tools/topo/hwloc/hwloc/config.log, as that was missing. I am using MPICH version 3.2.1, which is the latest stable release at the time of writing. > > > Thanks in advance for your help! > > > Best wishes, > > > Thomas Pak > > > _______________________________________________ > > > discuss mailing list discuss(a)mpich.org (mailto:[email protected]) > > > To manage subscription options or unsubscribe: > > > https://lists.mpich.org/mailman/listinfo/discuss > > > > > > > _______________________________________________ > > discuss mailing list discuss(a)mpich.org (mailto:[email protected]) > > To manage subscription options or unsubscribe: > > https://lists.mpich.org/mailman/listinfo/discuss > > > > > > > >

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Re: [mpich-discuss] MPI_Comm_spawn zombies have risen from the dead.
by Zhou, Hui 06 Dec '18

06 Dec '18

Hi Thomas, To summarize issue: MPICH proxy does not reap processes after its exit? I’ll look into the issue. From my peruse of current MPI standards, it does not really specify the behavior after MPI_Finalize. The dynamic process part of MPI support is weak, primary due to lack of application adoption. Regardless, I agree that the proxy creates the process should be responsible to reap its dead children. — Hui Zhou On Dec 6, 2018, at 3:53 AM, Thomas Pak via discuss <discuss(a)mpich.org<mailto:[email protected]>> wrote: Dear all, Does anyone have any feedback on this issue? The problem still persists in MPICH-3.3 and it seems like it is pointing to a severe flaw in how MPICH handles dynamic process creation. To reiterate, the following short program using MPICH creates zombie processes indefinitely until no more processes can be created. """ #include <stdio.h> #include <mpi.h> int main(int argc, char *argv[]) { // Initialize MPI MPI_Init(NULL, NULL); // Get parent MPI_Comm parent; MPI_Comm_get_parent(&parent); // If the process was not spawned if (parent == MPI_COMM_NULL) { puts("I was not spawned!"); // Spawn child process in loop char *cmd = argv[0]; char **cmd_argv = MPI_ARGV_NULL; int maxprocs = 1; MPI_Info info = MPI_INFO_NULL; int root = 0; MPI_Comm comm = MPI_COMM_SELF; MPI_Comm intercomm; int *array_of_errcodes = MPI_ERRCODES_IGNORE; for (;;) { MPI_Comm_spawn(cmd, cmd_argv, maxprocs, info, root, comm, &intercomm, array_of_errcodes); MPI_Comm_disconnect(&intercomm); } // If process was spawned } else { puts("I was spawned!"); MPI_Comm_disconnect(&parent); } // Finalize MPI_Finalize(); } """ Thanks in advance for your help. Best wishes, Thomas Pak On Oct 16 2018, at 4:57 pm, Thomas Pak <thomas.pak(a)maths.ox.ac.uk<mailto:[email protected]>> wrote: Dear all, My MPI application spawns a large number of MPI processes using MPI_Comm_spawn over its total lifetime. Unfortunately, I have experienced that this results in zombie processes of hydra_pmi_proxy accumulating over time. As a result, my MPI application will eventually crash because there are too many zombie processes and no new processes can be created. This issue does not seem to be new; I have found references to similar issues in at least three different places: - [mpich-discuss] MPI_Comm_Spawn causing zombies of hydra_pmi_proxy<https://lists.mpich.org/pipermail/discuss/2013-March/000599.html> (March 2013) - [GitHub issue] hydra_pmi_proxy zombie MPI_comm_spawn #1677<https://github.com/pmodels/mpich/issues/1677> (October 2016) - [Google Groups] Hanging in spawn in master-slave code and hydra_pmi_proxy zombies<https://groups.google.com/forum/#!msg/mpi4py/A9mN-2UkFf8/2gnUEtArDwAJ> (December 2016) In the first reference, a dirty fix was proposed by Silvan Brändli to simply reap all the zombie processes in a loop at the start of the function HYDU_create_process in src/pm/hydra/utils/launch/launch.c. However, I have found that this comes with its own set of problems and makes my MPI application unstable. In the GitHub issue, the problem was marked as "worksforme". However, this problem persists for me and other machines that I have tried to reproduce it on, so it clearly has not yet been resolved. In the Google Groups thread, the problem was "resolved" by avoiding spawning MPI processes entirely, which is not an option in my case. Pavan Balaji mentions in the 2013 mpi-discuss thread that this issue was a problem "once upon a time". It seems to have risen from the dead again. I have attached a short and self-contained program written in C that reproduces the problem. The program simply spawns child processes using MPI_Comm_spawn in an infinite loop, where each child process exits after writing a message to stdout. I use MPI_Comm_disconnect to disconnect the Intercommunicator, but the same problem occurs when using MPI_Comm_free instead. I have also attached the logfiles generated while building MPICH, as described in the README, except for the file mpich-3.2.1/src/pm/hydra/tools/topo/hwloc/hwloc/config.log, as that was missing. I am using MPICH version 3.2.1, which is the latest stable release at the time of writing. Thanks in advance for your help! Best wishes, Thomas Pak _______________________________________________ discuss mailing list discuss(a)mpich.org<mailto:[email protected]> To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss _______________________________________________ discuss mailing list discuss(a)mpich.org<mailto:[email protected]> To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Re: [mpich-discuss] MPI_Comm_spawn zombies have risen from the dead.
by Zhou, Hui 06 Dec '18

06 Dec '18

Hi Thomas, To summarize issue: MPICH proxy does not reap processes after its exit? I’ll look into the issue. From my peruse of current MPI standards, it does not really specify the behavior after MPI_Finalize. The dynamic process part of MPI support is weak, primary due to lack of application adoption. Regardless, I agree that the proxy creates the process should be responsible to reap its dead children. — Hui Zhou On Dec 6, 2018, at 3:53 AM, Thomas Pak via discuss <discuss(a)mpich.org<mailto:[email protected]>> wrote: Dear all, Does anyone have any feedback on this issue? The problem still persists in MPICH-3.3 and it seems like it is pointing to a severe flaw in how MPICH handles dynamic process creation. To reiterate, the following short program using MPICH creates zombie processes indefinitely until no more processes can be created. """ #include <stdio.h> #include <mpi.h> int main(int argc, char *argv[]) { // Initialize MPI MPI_Init(NULL, NULL); // Get parent MPI_Comm parent; MPI_Comm_get_parent(&parent); // If the process was not spawned if (parent == MPI_COMM_NULL) { puts("I was not spawned!"); // Spawn child process in loop char *cmd = argv[0]; char **cmd_argv = MPI_ARGV_NULL; int maxprocs = 1; MPI_Info info = MPI_INFO_NULL; int root = 0; MPI_Comm comm = MPI_COMM_SELF; MPI_Comm intercomm; int *array_of_errcodes = MPI_ERRCODES_IGNORE; for (;;) { MPI_Comm_spawn(cmd, cmd_argv, maxprocs, info, root, comm, &intercomm, array_of_errcodes); MPI_Comm_disconnect(&intercomm); } // If process was spawned } else { puts("I was spawned!"); MPI_Comm_disconnect(&parent); } // Finalize MPI_Finalize(); } """ Thanks in advance for your help. Best wishes, Thomas Pak On Oct 16 2018, at 4:57 pm, Thomas Pak <thomas.pak(a)maths.ox.ac.uk<mailto:[email protected]>> wrote: Dear all, My MPI application spawns a large number of MPI processes using MPI_Comm_spawn over its total lifetime. Unfortunately, I have experienced that this results in zombie processes of hydra_pmi_proxy accumulating over time. As a result, my MPI application will eventually crash because there are too many zombie processes and no new processes can be created. This issue does not seem to be new; I have found references to similar issues in at least three different places: - [mpich-discuss] MPI_Comm_Spawn causing zombies of hydra_pmi_proxy<https://lists.mpich.org/pipermail/discuss/2013-March/000599.html> (March 2013) - [GitHub issue] hydra_pmi_proxy zombie MPI_comm_spawn #1677<https://github.com/pmodels/mpich/issues/1677> (October 2016) - [Google Groups] Hanging in spawn in master-slave code and hydra_pmi_proxy zombies<https://groups.google.com/forum/#!msg/mpi4py/A9mN-2UkFf8/2gnUEtArDwAJ> (December 2016) In the first reference, a dirty fix was proposed by Silvan Brändli to simply reap all the zombie processes in a loop at the start of the function HYDU_create_process in src/pm/hydra/utils/launch/launch.c. However, I have found that this comes with its own set of problems and makes my MPI application unstable. In the GitHub issue, the problem was marked as "worksforme". However, this problem persists for me and other machines that I have tried to reproduce it on, so it clearly has not yet been resolved. In the Google Groups thread, the problem was "resolved" by avoiding spawning MPI processes entirely, which is not an option in my case. Pavan Balaji mentions in the 2013 mpi-discuss thread that this issue was a problem "once upon a time". It seems to have risen from the dead again. I have attached a short and self-contained program written in C that reproduces the problem. The program simply spawns child processes using MPI_Comm_spawn in an infinite loop, where each child process exits after writing a message to stdout. I use MPI_Comm_disconnect to disconnect the Intercommunicator, but the same problem occurs when using MPI_Comm_free instead. I have also attached the logfiles generated while building MPICH, as described in the README, except for the file mpich-3.2.1/src/pm/hydra/tools/topo/hwloc/hwloc/config.log, as that was missing. I am using MPICH version 3.2.1, which is the latest stable release at the time of writing. Thanks in advance for your help! Best wishes, Thomas Pak _______________________________________________ discuss mailing list discuss(a)mpich.org<mailto:[email protected]> To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss _______________________________________________ discuss mailing list discuss(a)mpich.org<mailto:[email protected]> To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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