[molpro-user] Permanent installation of dependencies

[Andy May]

Greg,

Glad to hear you got Molpro running. At the moment the auto-build 
options are marked as experimental, however the only known issue is the 
installation problem you mention. I'm not sure one can simply move 
mpich2/openmpi installation directories, but we will try to implement a 
solution.

Best wishes,

Andy

On 24/07/11 04:12, Gregory Magoon wrote:
> After some work I was finally able to trace this to some sort of issue between
> NFSv4 and MPICH2; I can get this to work properly when I mount the NFS drives
> as NFSv3 (as opposed to NFSv4), so the issue is now more-or-less resolved.
>
> A quick follow-up question: Is there a recommended approach for permanent
> installation of the mpich2 dependency (and maybe also GA?) when using the auto
> build approach? By default, it seems that the installation scripts leave the
> mpiexec in the compile directory. I saw that the makefile/installation scripts
> mention an option called REDIST which seemed like it might allow this,
> but they
> don't seem to make use of this option (REDIST=NO).
>
> Thanks,
> Greg
>
> Quoting Gregory Magoon<gmagoon at MIT.EDU>:
>
>> Hi,
>> I have successfully compiled molpro (with Global Arrays/TCGMSG; mpich2 from
>> Ubuntu package) on one of our compute nodes for our new server, and installed
>> it in an NFS directory on our head node. The initial tests on the
>> compute node
>> ran fine but since the installation, I've had issues with running
>> molpro on the
>> compute nodes (it seems to work fine on the head node). Sometimes
>> (sorry I can't
>> be more precise, but it does not seem to be reproducible), when
>> running on the
>> compute node, the job will get stuck in the early stages, producing a
>> lot (~14+
>> Mbps outbound to headnode and 7Mbps inbound from headnode) of NFS traffic and
>> causing fairly high nfsd process CPU% usage on the head node. Molpro
>> processes
>> in the stuck state are shown in "top" command display at the bottom of the
>> e-mail. I have also attached example verbose output for a case that
>> works and a
>> case that gets stuck.
>>
>> Some notes:
>> -/usr/local is mounted as NFS read-only file system; /home is mounted
>> as NFS rw
>> file system
>> -It seems like runs with fewer processors (e.g. 6) are more likely to run
>> successfully
>>
>> I've tried several approaches for addressing the issue, including 1. Mounting
>> /usr/local as rw file system, and 2. Changing the rsize and wsize parameters
>> for the NFS filesystem but none seem to work. We also tried piping<
>> /dev/null
>> when calling the process, which seemed like it was helping at first,
>> but later
>> tests suggested that this wasn't actually helping.
>>
>> If anyone has any tips or ideas to help diagnose the issue here, it would be
>> greatly appreciated. If there are any additional details I can
>> provide to help
>> describe the problem, I'd be happy to provide them.
>>
>> Thanks very much,
>> Greg
>>
>> Top processes in "top" output in stuck state:
>>   PID USER      PR  NI  VIRT  RES  SHR S %CPU %MEM    TIME+  COMMAND
>>    10 root      20   0     0    0    0 S   10  0.0   0:16.50 kworker/0:1
>>     2 root      20   0     0    0    0 S    6  0.0   0:10.86 kthreadd
>> 1496 root      20   0     0    0    0 S    1  0.0   0:04.73 kworker/0:2
>>     3 root      20   0     0    0    0 S    1  0.0   0:00.93 ksoftirqd/0
>>
>> Processes in "top" output for user in stuck state:
>>   PID USER      PR  NI  VIRT  RES  SHR S %CPU %MEM    TIME+  COMMAND
>> 29961 user      20   0 19452 1508 1072 R    0  0.0   0:00.05 top
>> 1176 user      20   0 91708 1824  868 S    0  0.0   0:00.01 sshd
>> 1177 user      20   0 24980 7620 1660 S    0  0.0   0:00.41 bash
>> 1289 user      20   0 91708 1824  868 S    0  0.0   0:00.00 sshd
>> 1290 user      20   0 24980 7600 1640 S    0  0.0   0:00.32 bash
>> 1386 user      20   0  4220  664  524 S    0  0.0   0:00.01 molpro
>> 1481 user      20   0 18764 1196  900 S    0  0.0   0:00.00 mpiexec
>> 1482 user      20   0 18828 1092  820 S    0  0.0   0:00.00 hydra_pmi_proxy
>> 1483 user      20   0 18860  488  212 D    0  0.0   0:00.00 hydra_pmi_proxy
>> 1484 user      20   0 18860  488  212 D    0  0.0   0:00.00 hydra_pmi_proxy
>> 1485 user      20   0 18860  488  212 D    0  0.0   0:00.00 hydra_pmi_proxy
>> 1486 user      20   0 18860  488  212 D    0  0.0   0:00.00 hydra_pmi_proxy
>> 1487 user      20   0 18860  488  212 D    0  0.0   0:00.00 hydra_pmi_proxy
>> 1488 user      20   0 18860  488  212 D    0  0.0   0:00.00 hydra_pmi_proxy
>> 1489 user      20   0 18860  488  212 D    0  0.0   0:00.00 hydra_pmi_proxy
>> 1490 user      20   0 18860  488  208 D    0  0.0   0:00.00 hydra_pmi_proxy
>> 1491 user      20   0 18860  488  208 D    0  0.0   0:00.00 hydra_pmi_proxy
>> 1492 user      20   0 18860  488  208 D    0  0.0   0:00.00 hydra_pmi_proxy
>> 1493 user      20   0 18860  488  208 D    0  0.0   0:00.00 hydra_pmi_proxy
>> 1494 user      20   0 18860  492  212 D    0  0.0   0:00.00 hydra_pmi_proxy
>>
>>
>>
>>
>
>
> _______________________________________________
> Molpro-user mailing list
> Molpro-user at molpro.net
> http://www.molpro.net/mailman/listinfo/molpro-user