Help running CP2K 5.1 jobs with Sungrid Engine queuing

Jerry Tanoury jerryt... at
Sat Feb 17 22:54:29 UTC 2018

I figured out the problem.  I had compiled fftw3 and libxc specifically 
setting 'F77=gfortran'.  I rebuilt them using the settings in the 
tools/toolchain/scripts.  This took care of the f77 error.  Then, I changed 
my input line in the submit script to explicitly call the number of nodes 
from mpirun:
"mpirun -np 4 
/cluster/home/tanoury/CP2K/cp2k-5.1/exe/CP2K_gnu-mkl/cp2k.popt ${1} > 

CP2K is running as expected.


On Friday, February 16, 2018 at 3:43:48 PM UTC-5, Jerry Tanoury wrote:
> Hi,
> I have successfully built a popt version of CP2K 5.1, and it passed all 
> regtests except for two.  The arch and error files are attached.  However, 
> when I try to run this on our cluster (SGE queuing), the job either 
> crashes, or only runs on 1 core when requesting 4 cores.  My submit script 
> is attached, as well as the error output file from SGE.  
> A few things about the submit script:
> - I source the intel compilers and libs, as well as openmpi before 
> submitting.  So, all required paths are passed to the nodes with #$ -V.
> - When I do not set OMPI_MCA_mpi_warn_on_fork 0, the job crashes with the 
> warning below.  
> --------------------------------------------------------------------------
> A process has executed an operation involving a call to the
> "fork()" system call to create a child process.  Open MPI is currently
> operating in a condition that could result in memory corruption or
> other system errors; your job may hang, crash, or produce silent
> data corruption.  The use of fork() (or system() or other calls that
> create child processes) is strongly discouraged.
> The process that invoked fork was:
>   Local host:          [[25312,1],0] (PID 5268)
> If you are *absolutely sure* that your application will successfully
> and correctly survive a call to fork(), you may disable this warning
> by setting the mpi_warn_on_fork MCA parameter to 0.
> --------------------------------------------------------------------------
> Is there anyone experienced with running CP2K jobs using SGE queuing?
> Does anyone have a SGE submit script that works, and/or do I need to set 
> up a unique pe for CP2K?
> Thank you for the help,
> Jerry
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <>

More information about the CP2K-user mailing list