I have tried running the Openmdao paraboloid tutorial as well as benchmarks and I consistently receive the same error which reads as following:
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[0]PETSC ERROR: to get more information on the crash
---------------------------------------------------------------------
MPI_abort was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 59.
NOTE: invoking MPI_ABORT causes MPI to kill all MPI processes.
you may or may not see output from other processes, depending on exactly when Open MPI kills them.
I don't understand why this error is occurring and what I can do to be able to run OpenMDAO without getting this error. Can you please help me with this?
Something has not gone well with your PETSc install. Its hard to debug that from afar though. It could be in your MPI install, or your PETSc install, or your petsc4py install. I suggest not install PETSc or PETSc4Py through pip though. I've had mixed success with that. Both can be installed from source without tremendous difficulty.
However, to run the tutorials you don't need to have PETSc installed. You could remove those packages and the tutorials will run correctly in serial for you
Related
I am trying to build GROMACS with icc compiler but it is throwing error I have provided the error below.
": internal error: 0_76
compilation aborted for /global/scratch/groups/hpcperf/2022_Refresh/gromacs/api/nblib/topology.cpp (code 4)
make[2]: *** [api/nblib/CMakeFiles/nblib.dir/build.make:216: api/nblib/CMakeFiles/nblib.dir/topology.cpp.o] Error 4
Any help appreciated!
A sample reproducer would help us resolve your issue from our end. However, GROMACS no longer supports Intel classic compilers (icc/icpc). It supports only the Intel LLVM compilers (icx/icpx).
I had the same issue and can confirm that it is resolved when switching from the classic compilers to the LLVM compilers. Note that if you use MPI, you also need to change the compiler for these wrappers, either via the I_MPI_CC(X) environment variable or the -cc / -cxx option.
Recently I installed Intel OneAPI including c compiler, FORTRAN compiler and mpi library and complied VASP with it.
Before presenting the question, there are some tricks I need to clarify during the installation of VASP:
GLIBC2.14: the cluster is an old machine with a glibc version of 2.12, where OneAPI needs a version of 2.14. So I compile the GLIBC2.14 and export the ld_path: export LD_LIBRARY_PATH="~/mysoft/glibc214/lib:$LD_LIBRARY_PATH"
ld 2.24: The ld version is 2.20 in the cluster, while a higher version is needed. So I installed binutils 2.24.
There is one master computer connected with 30 calculating nodes in the cluster. The calculation is executed with 3 ways:
When I do the calculation in the master, it's totally OK.
When I login the nodes manually with rsh command, the calculation in the logged node is also no problem.
But usually I submit the calculation script from the master (with slurm or pbs), and then do the calculation in the node. In that case, I met following error message:
[mpiexec#node3.alineos.net] poll_for_event (../../../../../src/pm/i_hydra/libhydra/demux/hydra_demux_poll.c:159): check exit codes error
[mpiexec#node3.alineos.net] HYD_dmx_poll_wait_for_proxy_event (../../../../../src/pm/i_hydra/libhydra/demux/hydra_demux_poll.c:212): poll for event error
[mpiexec#node3.alineos.net] HYD_bstrap_setup (../../../../../src/pm/i_hydra/libhydra/bstrap/src/intel/i_hydra_bstrap.c:1062): error waiting for event
[mpiexec#node3.alineos.net] HYD_print_bstrap_setup_error_message (../../../../../src/pm/i_hydra/mpiexec/intel/i_mpiexec.c:1015): error setting up the bootstrap proxies
[mpiexec#node3.alineos.net] Possible reasons:
[mpiexec#node3.alineos.net] 1. Host is unavailable. Please check that all hosts are available.
[mpiexec#node3.alineos.net] 2. Cannot launch hydra_bstrap_proxy or it crashed on one of the hosts. Make sure hydra_bstrap_proxy is available on all hosts and it has right permissions.
[mpiexec#node3.alineos.net] 3. Firewall refused connection. Check that enough ports are allowed in the firewall and specify them with the I_MPI_PORT_RANGE variable.
[mpiexec#node3.alineos.net] 4. pbs bootstrap cannot launch processes on remote host. You may try using -bootstrap option to select alternative launcher.
I only met this error with oneAPI compiled codes but Intel® Parallel Studio XE compiled. Do you have any idea of this error? Your response will be highly appreciated.
Best,
Léon
Could it be a permissions error with the Slurm agent not having the correct permissions or library path?
I'm really naive and know almost nothing about MPI. I'm trying to do some analyses in R that require Rmpi package. But I'm stuck with this problem:
Version of R 3.2.5 (x64) on Windows 10
I installed MPICH2
Added proper addresses on PATH environment variables
Successfully set smpd and mpiexec registration
Installed Rmpi using Rgui
If I call Rmpi using normal Rterm it is loaded. But when I try
mpi.spawn.Rslaves(), it returns :
Error in mpi.spawn.Rslaves() : Spawning is not implemented. Please use mpiexec with Rprofile.*
so I run on prompt :
mpiexec -n 2 "C:\Program Files\R\R-3.2.5\bin\x64\Rterm.exe" --no-save –q
So far so good.
I can load any package without problems but when it comes to call Rmpi library I get this error message:
Aborting: mpi appplication on DESKTOP-0UI5TAT is unable to connect to the smpd manager on (null):57362 error 1722
job aborted:
[ranks] message
[0] fatal error
Fatal error in MPI_Init: Other MPI error, error stack:
MPI_Init(argc_p=0x0018FA44, argv_p=0x0018FA48) failed
The RPC server is unavailable. (errno 1722)*
Even using the more recent MS-MPI software, when I call Rmpi it simply starts a new line without any prompt > and so it remains
I deep searched on the whole internet and tried several options but it's still not working
you have to create a shortcut that Rstudio is lunched by mpiexec ,otherwise the Rstudio doesn't know Mpi
follow instruction here
http://www.stats.uwo.ca/faculty/yu/Rmpi/
I am trying to run some OpenCL programs.
I have a NVidia graphics card (GeForce 6600).
But , when I execute my program and I get a error :
Unable to get platforms -1001
My OS is ArchLinux and I already install the following packages (
from pacman ):
1. libcl
2. opencl-headers
3. opencl-nvidia-304xx
4. lib32-opencl-nvidia-304xx
How to fix this problem in my environment？
or what necessary packages need to install?
thanks.
OpenCL-error -1001 "CL_PLATFORM_NOT_FOUND_KHR" doesn't necessarily mean you don't have any OpenCL-capable device. This means, that cl_khr_icd-extention have a trouble to load the proper vendor driver.
Try to run your OpenCL-program(s) as root. Or try to use clIcdGetPlatformIDsKHR.
If you not running X11, you need to create device files manually or by script
I've tried to run command in R 2.15.2
rsaga.geoprocessor(lib="ta_channels", module=0, param=list(ELEVATION="DEMflt.sgrd", CHNLNTWRK=paste("channels", i, ".sgrd", sep=""), CHNLROUTE="channel_route.sgrd", SHAPES="channels.shp", INIT_GRID="DEMflt.sgrd", DIV_CELLS=3, MINLEN=40), show.output.on.console=FALSE)
and I'm constantly getting this warning:
Warning message:
running command '"C:/Users/Nenad/Documents/R/win-library/2.15/RSAGA/SAGA-GIS/saga_cmd.exe" ta_preprocessor 2 -DEM "DEM1.sgrd" -RESULT "DEMflt.sgrd" -MINSLOPE "0.05"' had status 1
I use windows 8 and also tried to ran R as admin.
Any idea what is the problem? Thanks!
Idk how actual it is, but I've been struggling with "had status 1" warning a lot. Especially it got really annoying when I tried to use seasonal package to conduct the X13-ARIMA-SEATS seasonal decomposition of time series. The seasonal::seas command just didn't work, because in the code of this command there is a stop condition when running a certain stuff with cmd.exe returns non-zero status. While, as it was mentioned before, 'status 1' doesn't prevent command execution, in case of seasonal package it does.
The problem in my case was caused by some mistake in Windows Registry (Win 10), that in turn caused warning System cannot find the path specified when launching CMD.exe or PowerShell, which caused warning inside R as well. So to fix it:
Press Win+R -> regedit
In HKEY_CURRENT_USER\SOFTWARE\Microsoft\Command Processor folder clean the value of Autorun record (it should be empty)
Do the same for Autorun in HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Command Processor
After these actions annoying warning with "has status 1" has gone and seasonal::seas started to work perfectly.
Hope it will be usefull for somebody.
Running system commands from R can be really tricky. In my experience, as long as the exit code is not 127 then the command did run, and you could use the intern=TRUE switch in the system command for a more verbose output. If you run the command again, the warning message could contain a errmsg attribute as well for some more info. hth