Re: AW: namd 2.9 not going so well

From: Michael Galloway (gallowaymd_at_ornl.gov)
Date: Mon Sep 17 2012 - 07:16:59 CDT

i did check those parameters, they were set as required:

[root_at_cmbcluster ~]# fornodes "cat /sys/class/net/ib0/mtu"
==================== node001 ====================
65520
==================== node002 ====================
65520
==================== node003 ====================
65520
==================== node004 ====================
65520
...

[root_at_cmbcluster ~]# fornodes "cat /sys/class/net/ib0/mode"
==================== node001 ====================
connected
==================== node002 ====================
connected
==================== node003 ====================
connected
==================== node004 ====================
connected
==================== node005 ====================
connected
==================== node006 ====================
connected
....

On 09/17/2012 02:00 AM, Norman Geist wrote:
> Hi Micheal,
>
> have you set the mode and mtu settings for IPoIB like I turned out?
>
> Just do for ib0
>
> echo "connected" > /sys/class/net/ib0/mode
> echo "65520" > /sys/class/net/ib0/mtu
>
> fit the commands if you have other names for your interface or another shell
> than bash. This should give you the expected performance. In the
> compatibility mode "datagram" (check with cat /sys/class/net/ib0/mode) the
> performance is comparable with standard Gigabit Ethernet only.
>
> Regards
>
> Norman Geist.
>
>> -----Ursprüngliche Nachricht-----
>> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
>> Auftrag von Michael Galloway
>> Gesendet: Donnerstag, 13. September 2012 17:30
>> An: namd-l
>> Betreff: namd-l: namd 2.9 not going so well
>>
>> ok, i've been experimenting with namd built with openmpi and running
>> binaries over IPoIB and its not going so well.
>>
>> my namd2.9 built with gcc 4.7.1 and the apoa1 test data with 4 nodes by
>> 12 cores per node is:
>>
>> [mgx_at_cmbcluster namd]$ mpirun -np 48 -machinefile nodes
>> /shared/namd-2.9-gcc471/Linux-x86_64-g++/namd2 apoa1/apoa1.namd
>>
>>
>> Info: Benchmark time: 48 CPUs 0.0357351 s/step 0.413601 days/ns 309.887
>> MB memory
>> TIMING: 500 CPU: 19.0964, 0.0354278/step Wall: 19.0964,
>> 0.0354278/step, 0 hours remaining, 309.886719 MB of memory in use.
>> ETITLE: TS BOND ANGLE DIHED
>> IMPRP ELECT VDW BOUNDARY MISC
>> KINETIC TOTAL TEMP POTENTIAL TOTAL3
>> TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG
>> GPRESSAVG
>>
>> ENERGY: 500 20974.8940 19756.6571 5724.4523
>> 179.8271 -337741.4155 23251.1001 0.0000 0.0000
>> 45359.0760 -222495.4090 165.0039 -267854.4849
>> -222061.0908 165.0039 -3197.5171 -2425.4142
>> 921491.4634 -3197.5171 -2425.4142
>>
>> WRITING EXTENDED SYSTEM TO OUTPUT FILE AT STEP 500
>> WRITING COORDINATES TO OUTPUT FILE AT STEP 500
>> The last position output (seq=-2) takes 0.002 seconds, 315.496 MB of
>> memory in use
>> WRITING VELOCITIES TO OUTPUT FILE AT STEP 500
>> The last velocity output (seq=-2) takes 0.002 seconds, 315.496 MB of
>> memory in use
>> ====================================================
>>
>> WallClock: 20.894575 CPUTime: 20.894575 Memory: 315.496094 MB
>> End of program
>>
>> same dataset, same node processor count for the NAMD_2.9_Linux-x86_64
>> binary run over IBoIP:
>>
>> [mgx_at_cmbcluster NAMD_2.9_Linux-x86_64]$ ./charmrun ./namd2 +p48
>> ++nodelist ./nodelist ++remote-shell ssh apoa1/apoa1.namd
>>
>> Info: Benchmark time: 48 CPUs 0.278276 s/step 3.22078 days/ns 54.4712
>> MB
>> memory
>> TIMING: 500 CPU: 17.0394, 0.0332949/step Wall: 120.797,
>> 0.246653/step,
>> 0 hours remaining, 54.471237 MB of memory in use.
>> ETITLE: TS BOND ANGLE DIHED
>> IMPRP ELECT VDW BOUNDARY MISC
>> KINETIC TOTAL TEMP POTENTIAL TOTAL3
>> TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG
>> GPRESSAVG
>>
>> ENERGY: 500 20974.8941 19756.6576 5724.4523
>> 179.8271 -337741.4179 23251.1005 0.0000 0.0000
>> 45359.0770 -222495.4094 165.0039 -267854.4864
>> -222061.0912 165.0039 -3197.5171 -2425.4143
>> 921491.4634 -3197.5171 -2425.4143
>>
>> WRITING EXTENDED SYSTEM TO OUTPUT FILE AT STEP 500
>> WRITING COORDINATES TO OUTPUT FILE AT STEP 500
>> The last position output (seq=-2) takes 0.003 seconds, 59.168 MB of
>> memory in use
>> WRITING VELOCITIES TO OUTPUT FILE AT STEP 500
>> The last velocity output (seq=-2) takes 0.004 seconds, 59.014 MB of
>> memory in use
>> ====================================================
>>
>> WallClock: 141.985214 CPUTime: 21.389748 Memory: 59.014664 MB
>>
>> i still get random segfaults with my compiled namd :-\

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