Problem in running parallel yt on stampede
Dear yt-users, I'm trying to use parallel yt on stampede and got this error -- LiMIC: (limic_open) file open fail [unset]: aborting job: Fatal error in PMPI_Init_thread: Other MPI error, error stack: MPIR_Init_thread(436)....: MPID_Init(371)...........: channel initialization failed MPIDI_CH3_Init(335)......: MPIDI_CH3I_SMP_Init(1723): LiMIC2 device does not exist: No such file or directory In the interactive ipython, import yt and import mpi4py works ok but, yt.enable_parallelism() gives the same error. Serial scripts runs perfectly fine. I've also tried building mpi4py by specifying mpicc path; itdoesn't work. Any help would be highly appreciated. Thanks in advance. rahul
How did mpi4py get installed? You may need to troubleshoot this with the Stampede sysadmins, since the error is being raised by the MPI library you're using. On Sunday, July 5, 2015, rahul kashyap <rahulkashyap411@gmail.com> wrote:
Dear yt-users,
I'm trying to use parallel yt on stampede and got this error -- LiMIC: (limic_open) file open fail [unset]: aborting job: Fatal error in PMPI_Init_thread: Other MPI error, error stack: MPIR_Init_thread(436)....: MPID_Init(371)...........: channel initialization failed MPIDI_CH3_Init(335)......: MPIDI_CH3I_SMP_Init(1723): LiMIC2 device does not exist: No such file or directory
In the interactive ipython, import yt and import mpi4py works ok but, yt.enable_parallelism() gives the same error. Serial scripts runs perfectly fine. I've also tried building mpi4py by specifying mpicc path; itdoesn't work.
Any help would be highly appreciated. Thanks in advance.
rahul
Are you running on the login node? I've seen this too when I try to use mpi4py in a script on the Stampede login ode. Specifically, it fails in the 'from mpi4py import MPI' step. This happens even if I am not using yt or not running in parallel. mpi4py works fine (for me at least) in an interactive compute node. I wonder if they have the login nodes set up to discourage parallel jobs. -- Greg On Sun, Jul 5, 2015 at 7:02 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
How did mpi4py get installed?
You may need to troubleshoot this with the Stampede sysadmins, since the error is being raised by the MPI library you're using.
On Sunday, July 5, 2015, rahul kashyap <rahulkashyap411@gmail.com> wrote:
Dear yt-users,
I'm trying to use parallel yt on stampede and got this error -- LiMIC: (limic_open) file open fail [unset]: aborting job: Fatal error in PMPI_Init_thread: Other MPI error, error stack: MPIR_Init_thread(436)....: MPID_Init(371)...........: channel initialization failed MPIDI_CH3_Init(335)......: MPIDI_CH3I_SMP_Init(1723): LiMIC2 device does not exist: No such file or directory
In the interactive ipython, import yt and import mpi4py works ok but, yt.enable_parallelism() gives the same error. Serial scripts runs perfectly fine. I've also tried building mpi4py by specifying mpicc path; itdoesn't work.
Any help would be highly appreciated. Thanks in advance.
rahul
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participants (3)
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Greg Meece -
Nathan Goldbaum -
rahul kashyap