Re: [OMPI users] job aborts "readv failed: Connection reset by peer"

2016-09-02 Thread Gilles Gouaillardet
you need to run the ulimit command before mpirun and on the same node. if it still does not work, then you can use a wrapper. instead of mpirun a.out you would do mpirun a.sh a.sh is a script ulimit -c unlimited exec a.out the core is created in the current directory Cheers, Gilles On

Re: [OMPI users] Error in file runtime/orte_init.c

2016-09-02 Thread Mahmood Naderan
‚ÄčOK thanks for the hint. In fact 'ldd' command shows that some libraries were missing. adding the paths to LD_LIBRARY_PATH solved the problem. Regards, Mahmood ___ users mailing list users@lists.open-mpi.org

Re: [OMPI users] Error in file runtime/orte_init.c

2016-09-02 Thread Jeff Squyres (jsquyres)
Did you, perchance, install open MPI v2.0.0 in the same directory tree that a prior version of open MPI was already installed? If so, open MPI may be trying to use plugins from the prior version of open MPI, which will be problematic. Sent from my phone. No type good. > On Sep 2, 2016, at

Re: [OMPI users] job aborts "readv failed: Connection reset by peer"

2016-09-02 Thread Jeff Squyres (jsquyres)
Note that open MPI v2.0.0 is not ABI compatible with prior releases of open MPI. If you are trying to run an MPI executable created by a prior version of open MPI, you will need to recompile your application with open MPI v2.0.0. Sent from my phone. No type good. > On Sep 2, 2016, at 12:48

Re: [OMPI users] job aborts "readv failed: Connection reset by peer"

2016-09-02 Thread Mahmood Naderan
Thanks for your help. Please see below mahmood@compute-0-1:~$ ldd /share/apps/chemistry/siesta-3.2-pl-5/tpar/transiesta linux-vdso.so.1 => (0x7fffba9a8000) libmpi_f90.so.1 => /opt/openmpi/lib/libmpi_f90.so.1 (0x2b472b64) libmpi_f77.so.1 =>

Re: [OMPI users] job aborts "readv failed: Connection reset by peer"

2016-09-02 Thread John Hearns via users
Thankyou. That is helpful. Could you run an 'ldd' on your executable, on one of the compute nodes if possible? I will nto be able to solve your problem, but at least we now know what the application is, and can look at the libraries it is using. On 2 September 2016 at 17:19, Mahmood Naderan

Re: [OMPI users] job aborts "readv failed: Connection reset by peer"

2016-09-02 Thread Mahmood Naderan
The application is Siesta-3.2 and the command I use is /share/apps/computer/openmpi-1.6.5/bin/mpirun -hostfile hosts.txt -np 15 /share/apps/chemistry/siesta-3.2-pl-5/tpar/transiesta < trans-cc-bt-cc-163-20.fdf There is one node in the hosts.txt file. I have built transiesta binary from the

Re: [OMPI users] job aborts "readv failed: Connection reset by peer"

2016-09-02 Thread John Hearns via users
Mahmood, are you compiling and linking this application? Or are you using an executable which someone else has prepared? It would be very useful if we could know the application. On 2 September 2016 at 16:35, Mahmood Naderan wrote: > >Did you ran > >ulimit -c unlimited

[OMPI users] Error in file runtime/orte_init.c

2016-09-02 Thread Mahmood Naderan
Hi, Using OpenMPI-2.0.0, is there any idea about this error A requested component was not found, or was unable to be opened. This means that this component is either not installed or is unable to be used on your system (e.g., sometimes this means that shared libraries that the component requires

Re: [OMPI users] job aborts "readv failed: Connection reset by peer"

2016-09-02 Thread Mahmood Naderan
>Did you ran >ulimit -c unlimited >before invoking mpirun ? Yes. On the node which says that error. Is that file created in the current working directory? Or it is somewhere in the system folders? As another question, I am trying to use OpenMPI-2.0.0 as a new one. Problem is that the

Re: [OMPI users] New to (Open)MPI

2016-09-02 Thread Dave Goodell (dgoodell)
Lachlan mentioned that he has "M Series" hardware, which, to the best of my knowledge, does not officially support usNIC. It may not be possible to even configure the relevant usNIC adapter policy in UCSM for M Series modules/chassis. Using the TCP BTL may be the only realistic option here.

Re: [OMPI users] New to (Open)MPI

2016-09-02 Thread Jeff Squyres (jsquyres)
Greetings Lachlan. Yes, Gilles and John are correct: on Cisco hardware, our usNIC transport is the lowest latency / best HPC-performance transport. I'm not aware of any MPI implementation (including Open MPI) that has support for FC types of transports (including FCoE). I'll ping you

Re: [OMPI users] job aborts "readv failed: Connection reset by peer"

2016-09-02 Thread Jeff Squyres (jsquyres)
Also, the error message suggested that TCP is not the issue here -- the TCP hangups are likely because some other process exited unexpectedly. Indeed: - mpirun noticed that process rank 0 with PID 4989 on node compute-0-1 exited on signal 4 (Illegal instruction). - This might be the

Re: [OMPI users] job aborts "readv failed: Connection reset by peer"

2016-09-02 Thread John Hearns via users
Mahmood, as Giles says start by looking at how that application is compiled and linked. Run 'ldd' on the executable and look closely at the libraries. Do this on a compute node if you can. There was a discussion on another mailign list recently about how to fingerpritn executables and see which

Re: [OMPI users] job aborts "readv failed: Connection reset by peer"

2016-09-02 Thread Gilles Gouaillardet
Did you ran ulimit -c unlimited before invoking mpirun ? if your application can be ran with only one tasks, you can try to run it under gdb. you will hopefully be able to see where the illegal instruction occurs. since you are running on AMD processors, you have to make sure you are not using

Re: [OMPI users] job aborts "readv failed: Connection reset by peer"

2016-09-02 Thread Mahmood Naderan
>Are you running under a batch manager ? >On which architecture ? Currently I am not using the job manager (which is actually PBS). I am running from the terminal. The machines are AMD Opteron 64 bit >Hopefully you will get a core file that points you to the illegal instruction Where is that

Re: [OMPI users] New to (Open)MPI

2016-09-02 Thread John Hearns via users
Hello Lachlan. I think Jeff Squyres will be along in a short while! HE is of course the expert on Cisco. In the meantime a quick Google turns up: http://www.cisco.com/c/en/us/td/docs/unified_computing/ucs/usnic/c/deployment/2_0_X/b_Cisco_usNIC_Deployment_Guide_For_Standalone_C-SeriesServers.html