[Wien] k-point parallelization in WIEN2K_09.1
Peter Blaha
pblaha at theochem.tuwien.ac.at
Wed Jun 16 16:26:13 CEST 2010
No, there was no change!
Did you set "shared memory" ?? This would also explain why everything runs on
one machine ??
Kakhaber Jandieri schrieb:
> Dear prof. Blaha
>
>> I do NOT believe that k-point parallel with an older WIEN2k was possible
>> (unless you set it up with "rsh" instead of "ssh" and defined a
>> .rhosts file).
>
> But it is really possible. I checked again. I even reinstall the
> WIEN2K_08.1 aiming to verify that the options are the same as that used
> for WIEN2K_09.1.
> I did not set "rsh" and did not define ".rhost file.
> The behaviour of WIEN2K_08.1 is the same (as I described in my previous
> letters).
> According to dayfile, k-points are distributed among all reserved nodes.
> Here is a little fragment of the dayfile:
>
>
> Calculating GaAsB in /home/kakhaber/wien_work/GaAsB
> on node112 with PID 10597
>
> start (Wed Jun 16 09:50:23 CEST 2010) with lapw0 (40/99 to go)
>
> cycle 1 (Wed Jun 16 09:50:23 CEST 2010) (40/99 to go)
>
>> lapw0 -p (09:50:23) starting parallel lapw0 at Wed Jun 16
>> 09:50:23 CEST 2010
> --------
> running lapw0 in single mode
> 77.496u 0.628s 1:18.47 99.5% 0+0k 0+7008io 0pf+0w
>> lapw1 -c -p (09:51:42) starting parallel lapw1 at Wed Jun 16
>> 09:51:42 CEST 2010
> -> starting parallel LAPW1 jobs at Wed Jun 16 09:51:42 CEST 2010
> running LAPW1 in parallel mode (using .machines)
> 4 number_of_parallel_jobs
> node112(1) 2091.6u 2.3s 37:18.76 93.5% 0+0k 0+205296io 0pf+0w
> node105(1) 2024.2u 2.3s 34:26.54 98.0% 0+0k 0+198376io 0pf+0w
> node122(1) 2115.4u 5.1s 36:08.08 97.8% 0+0k 0+197808io 0pf+0w
> node131(1) 2041.3u 2.6s 35:19.70 96.4% 0+0k 0+202912io 0pf+0w
> Summary of lapw1para:
> node112 k=1 user=2091.6 wallclock=2238.76
> node105 k=1 user=2024.2 wallclock=2066.54
> node122 k=1 user=2115.4 wallclock=2168.08
> node131 k=1 user=2041.3 wallclock=2119.7
> 8274.113u 15.744s 37:20.53 369.9% 0+0k 8+805440io 0pf+0w
>> lapw2 -c -p (10:29:02) running LAPW2 in parallel mode
> node112 87.4u 0.5s 1:37.85 89.9% 0+0k 0+8104io 0pf+0w
> node105 86.8u 0.9s 1:30.90 96.5% 0+0k 198064+8096io 0pf+0w
> node122 84.7u 0.6s 1:27.71 97.3% 0+0k 0+8088io 0pf+0w
> node131 87.9u 1.0s 1:31.00 97.7% 0+0k 0+8088io 0pf+0w
> Summary of lapw2para:
> node112 user=87.4 wallclock=97.85
> node105 user=86.8 wallclock=90.9
> node122 user=84.7 wallclock=87.71
> node131 user=87.9 wallclock=91
> 349.001u 3.592s 1:41.96 345.8% 0+0k 204504+42240io 0pf+0w
>> lcore (10:30:44) 0.176u 0.060s 0:01.05 21.9% 0+0k 0+5336io 0pf+0w
>> mixer (10:30:46) 1.436u 0.168s 0:01.99 79.8% 0+0k 0+11920io
>> 0pf+0w
> :ENERGY convergence: 0 0.001 0
> :CHARGE convergence: 0 0.001 0
> ec cc and fc_conv 0 0 0
>
> In spite of that, when I login into the nodes, I see the following:
>
> node112:~> nice top -c -u kakhaber (this is the master node)
>
> top - 10:58:42 up 116 days, 23:19, 1 user, load average: 8.01, 7.77, 7.33
> Tasks: 110 total, 10 running, 100 sleeping, 0 stopped, 0 zombie
> Cpu(s): 90.5%us, 0.3%sy, 9.1%ni, 0.0%id, 0.0%wa, 0.0%hi, 0.0%si,
> 0.0%st
> Mem: 16542480k total, 16144412k used, 398068k free, 105896k buffers
> Swap: 4000144k total, 18144k used, 3982000k free, 11430460k cached
>
> PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND
> 14474 kakhaber 20 0 937m 918m 2020 R 100 5.7 26:06.48 lapw1c
> lapw1_4.def
> 14458 kakhaber 20 0 926m 907m 2020 R 98 5.6 26:01.62 lapw1c
> lapw1_3.def
> 14443 kakhaber 20 0 934m 915m 2028 R 98 5.7 25:46.37 lapw1c
> lapw1_2.def
> 14428 kakhaber 20 0 936m 917m 2028 R 66 5.7 24:26.43 lapw1c
> lapw1_1.def
> 5952 kakhaber 20 0 13724 1360 820 S 0 0.0 0:00.00 /bin/tcsh
> /var/spoo
> 6077 kakhaber 20 0 3920 736 540 S 0 0.0 0:00.00 /bin/csh -f
> /home/k
> 10597 kakhaber 20 0 3928 780 572 S 0 0.0 0:00.00 /bin/csh -f
> /home/k
> 14320 kakhaber 20 0 11252 1180 772 S 0 0.0 0:00.00 /bin/tcsh
> -f /home/
> 14336 kakhaber 20 0 3920 800 604 S 0 0.0 0:00.62 /bin/csh -f
> /home/k
> 14427 kakhaber 20 0 3920 440 244 S 0 0.0 0:00.00 /bin/csh -f
> /home/k
> 14442 kakhaber 20 0 3920 432 236 S 0 0.0 0:00.00 /bin/csh -f
> /home/k
> 14457 kakhaber 20 0 3920 432 236 S 0 0.0 0:00.00 /bin/csh -f
> /home/k
> 14472 kakhaber 20 0 3920 432 236 S 0 0.0 0:00.00 /bin/csh -f
> /home/k
> 16499 kakhaber 20 0 77296 1808 1100 R 0 0.0 0:00.00 sshd:
> kakhaber at pts/
> 16500 kakhaber 20 0 16212 2032 1080 S 0 0.0 0:00.02 -tcsh
> 16603 kakhaber 24 4 10620 1120 848 R 0 0.0 0:00.02 top -c -u
> kakhaber
>
>
> node105:~> nice top -c -u kakhaber
> top - 11:01:37 up 116 days, 23:23, 1 user, load average: 3.00, 3.00, 3.00
> Tasks: 99 total, 3 running, 96 sleeping, 0 stopped, 0 zombie
> Cpu(s): 2.9%us, 20.6%sy, 49.9%ni, 25.0%id, 0.0%wa, 0.1%hi, 1.6%si,
> 0.0%st
> Mem: 16542480k total, 6277020k used, 10265460k free, 233364k buffers
> Swap: 4000144k total, 13512k used, 3986632k free, 5173312k cached
>
> PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND
> 18955 kakhaber 20 0 77296 1808 1100 S 0 0.0 0:00.00 sshd:
> kakhaber at pts/
> 18956 kakhaber 20 0 16212 2032 1080 S 0 0.0 0:00.02 -tcsh
> 19071 kakhaber 24 4 10620 1112 848 R 0 0.0 0:00.00 top -c -u
> kakhaber
>
> for node122 and node131 the output is the same as for node105.
>
>> Anyway, k-parallel does not use mpi at all and you have to read the
>> requirements specified in the UG.
>
> I know, but I meant the following: if k-point parallelization in
> WIEN2K_09.1 does not work because of the problem with interconnection
> between different nodes, then I thought that the MPI-parallelization
> also should be impossible. But the MPI-parallel jobs runs without any
> problem.
>
> I suggest one possibility (may be trivial or wrong).
> In WIEN2K_08.1 k-point parallelization works but all processes run on
> the master node. In WIEN2K_09.1 k-point parallelization does not work at
> all. May be there is some restriction in WIEN2K_09.1 preventing
> different k-processes to be ran on the same node and this is the reason
> of the crash in parallel lapw1?
>
> Is such suggestion reasonable?
> I will be extremely thankful for your additional advices.
>
>
>> Kakhaber Jandieri schrieb:
>>> Dear Prof. Blaha,
>>>
>>> Thank you for your reply.
>>>
>>>> Can you ssh node120 ps
>>>> without supplying a password ?
>>>
>>> No, I can't ssh the nodes without password supply, but in my
>>> parallel_options I have setenv MPI_REMOTE 0. I thought that our
>>> cluster has a shared memory architecture, since the
>>> MPI-parallelization works without any problem for 1 k-point. I
>>> cheeked the corresponding nodes. All they were loaded. May be I
>>> misunderstood something. Are the requirements for
>>> MPI-parallelization different from that for k-point paralleization?
>>>
>>>> Try x lapw1 -p on the commandline.
>>>> What exactly is the "error" ?
>>>
>>> Just now, to try your suggestions, I ran new task with k-point
>>> parallelization. The .machines file is:
>>> granularity:1
>>> 1:node120
>>> 1:node127
>>> 1:node121
>>> 1:node123
>>>
>>> with node120 as a master node.
>>>
>>> The output of x lapw -p is:
>>> starting parallel lapw1 at Sun Jun 13 22:44:08 CEST 2010
>>> -> starting parallel LAPW1 jobs at Sun Jun 13 22:44:08 CEST 2010
>>> running LAPW1 in parallel mode (using .machines)
>>> 4 number_of_parallel_jobs
>>> [1] 31314
>>> [2] 31341
>>> [3] 31357
>>> [4] 31373
>>> Permission denied, please try again.
>>> Permission denied, please try again.
>>> Received disconnect from 172.26.6.120: 2: Too many authentication
>>> failures for kakhaber
>>> [1] Done ( ( $remote $machine[$p] ...
>>> Permission denied, please try again.
>>> Permission denied, please try again.
>>> Received disconnect from 172.26.6.127: 2: Too many authentication
>>> failures for kakhaber
>>> Permission denied, please try again.
>>> Permission denied, please try again.
>>> Received disconnect from 172.26.6.121: 2: Too many authentication
>>> failures for kakhaber
>>> [3] - Done ( ( $remote $machine[$p] ...
>>> [2] - Done ( ( $remote $machine[$p] ...
>>> Permission denied, please try again.
>>> Permission denied, please try again.
>>> Received disconnect from 172.26.6.123: 2: Too many authentication
>>> failures for kakhaber
>>> [4] Done ( ( $remote $machine[$p] ...
>>> node120(1) node127(1) node121(1) node123(1) **
>>> LAPW1 crashed!
>>> cat: No match.
>>> 0.116u 0.324s 0:11.88 3.6% 0+0k 0+864io 0pf+0w
>>> error: command /home/kakhaber/WIEN2K_09/lapw1cpara -c lapw1.def
>>> failed
>>>
>>>> How many k-points do you have ? ( 4 ?)
>>>
>>> Yes, I have 4 k-points.
>>>
>>>> Content of .machine1 and .processes
>>>
>>> marc-hn:~/wien_work/GaAsB> cat .machine1 node120
>>> marc-hn:~/wien_work/GaAsB> cat .machine2
>>> node127
>>> marc-hn:~/wien_work/GaAsB> cat .machine3
>>> node121
>>> marc-hn:~/wien_work/GaAsB> cat .machine4
>>> node123
>>>
>>> marc-hn:~/wien_work/GaAsB> cat .processes
>>> init:node120
>>> init:node127
>>> init:node121
>>> init:node123
>>> 1 : node120 : 1 : 1 : 1
>>> 2 : node127 : 1 : 1 : 2
>>> 3 : node121 : 1 : 1 : 3
>>> 4 : node123 : 1 : 1 : 4
>>>
>>>> While x lapw1 -p is running, do a ps -ef |grep lapw
>>>
>>> I had not enough time to do it - the program crashed before.
>>>
>>>> Your .machines file is most likely a rather "useless" one. The
>>>> mpi-lapw1
>>>> diagonalization (SCALAPACK) is almost a factor of 2 slower than the
>>>> serial
>>>> version, thus your speedup by using 2 processors in mpi-mode will be
>>>> very small.
>>>
>>> Yes, I know, but I am simply trying to arrange the calculations
>>> using Wien2K. For "real" calculations I will use much more processors.
>>>
>>> And finally, for additional information. As I wrote in my previous
>>> letters, in
>>> WIEN2k_08.1 k-point parallelization works, but all processes are
>>> running on master node and all other reserved nodes are idle. I
>>> forgot to mention: this is true for lapw1 only. Lapw2 is distributed
>>> among all reserved nodes.
>>>
>>> Thank you one again. I am looking forward for your further advices.
>>>
>>>
>>> Dr. Kakhaber Jandieri
>>> Department of Physics
>>> Philipps University Marburg
>>> Tel:+49 6421 2824159 (2825704)
>>>
>>>
>>> _______________________________________________
>>> Wien mailing list
>>> Wien at zeus.theochem.tuwien.ac.at
>>> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
>>
>> --
>> -----------------------------------------
>> Peter Blaha
>> Inst. Materials Chemistry, TU Vienna
>> Getreidemarkt 9, A-1060 Vienna, Austria
>> Tel: +43-1-5880115671
>> Fax: +43-1-5880115698
>> email: pblaha at theochem.tuwien.ac.at
>> -----------------------------------------
>> _______________________________________________
>> Wien mailing list
>> Wien at zeus.theochem.tuwien.ac.at
>> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
>
>
>
> Dr. Kakhaber Jandieri
> Department of Physics
> Philipps University Marburg
> Tel:+49 6421 2824159 (2825704)
>
>
> _______________________________________________
> Wien mailing list
> Wien at zeus.theochem.tuwien.ac.at
> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
--
P.Blaha
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Phone: +43-1-58801-15671 FAX: +43-1-58801-15698
Email: blaha at theochem.tuwien.ac.at WWW: http://info.tuwien.ac.at/theochem/
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