Firefly and PC GAMESS-related discussion club

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Alex Granovsky
gran@classic.chem.msu.su

Check (using ldd) that Firefly is indeed using mpich2 version of libmpich.so.1.1

E.g., on our systems:

[root@duath2]# ldd ./firefly
   linux-gate.so.1 =>  (0x00370000)
   libm.so.6 => /lib/libm.so.6 (0x492c2000)
   libmpich.so.1.1 => /opt/mpich2/lib/libmpich.so.1.1 (0x00111000)
   libpthread.so.0 => /lib/libpthread.so.0 (0x492f1000)
   librt.so.1 => /lib/librt.so.1 (0x49465000)
   libc.so.6 => /lib/libc.so.6 (0x49183000)
   /lib/ld-linux.so.2 (0x487b4000)

Next, check if mpiexec you are running is of mpich2 distribution.

Finally, the correct command line (as was already discussed several times) would be something like:

mpiexec -np 16 /home/mirix/Downloads/firefly/firefly -r -f -p -stdext -i /home/mirix/jobs/test.inp -o /home/mirix/jobs/test.out -ex /home/mirix/Downloads/firefly -t /disk/scratch/firefly/job1

Regards,
Alex




On Mon Jun 21 '10 1:53am, Miro Moman wrote
------------------------------------------
>Dear Alex,

>Thanks for your advice. However, I am still not able to have Firefly propagating.

>I have added  $smp httfix=.f. smppar=.t. $end  to the input file.

>This is the command line I am using now:

>mpiexec -np 16 /home/mirix/Downloads/firefly/firefly_71g_linux_mpich2_p4/firefly -t /disk/scratch/pcgamess/ -ncores 8 -nthreads 2

>I have tried different values for -np, -ncores and -nthreads, including removing those options entirely. I have also tried mpirun.

>Each time only one virtual core is used (half of a physical core). Eventually, I was able to have Firefly running on two virtual cores... but that is all.

>Best regards,

>Miro
>
>
>On Sun Jun 20 '10 10:39pm, Alex Granovsky wrote
>-----------------------------------------------
>>Hi,

>>you are using wrong command line syntax.
>>Firefly requires use of fully qualified filenames
>>in the command line. Moreover, if you are using the
>>old-style command line syntax passing directories
>>list at the end of command line, you should specify
>>exactly one directory per each process, and all these
>>directories MUST exist prior to Firefly's run.

>>So, please check the documentation on command line options.

>>One addition comment concerning your run.
>>If you are going to run 16 Firefly instances
>>on all 16 logical cores of your dual-cpu/eight-core
>>system, add the following line to your input:

>>

 $smp httfix=.f. smppar=.t. $end      

>>Without this line, FF will affinitize (bind to cores)
>>itself in such a way so that only half of all logical
>>cores will be in use; and thus, you'll effectively run
>>16 processes using only 8 logical cores.

>>Regards,
>>Alex Granovsky
>>
>>
>>
>>On Sun Jun 20 '10 8:41pm, Miro Moman wrote
>>------------------------------------------
>>>More info:

>>>If I run:

>>>mpiexec -np 16 /home/mirix/Downloads/firefly/firefly_71g_linux_mpich2_p4/firefly -i complex.inp -o output.out /disk/scratch/pcgamess /tmp/pcgamess

>>>The program does not run and I obtain:

>>> FATAL ERROR INITIALIZING FIREFLY! CHECK YOUR COMMAND LINE OPTIONS!

>>> ON MASTER NODE, ERROR CODE IS : 0x00000004
>>>    Unable to create output file

>>>If I remove the "-o output.out" option, the program runs, but the end of the output file reads:

>>>    2000000 WORDS OF MEMORY AVAILABLE

>>> Warning: running without fastdiag runtime extension!

>>> Warning: HTT is enabled, bitmask of physically unique cores is 0x0000FF00

>>> SMT aware parts of program will use              2 threads.

>>> Creating thread pool to serve up to            128 threads.

>>> Activating Call64 option.

>>> Using 64-bit DGEMM by default.
>>> **** ERROR, NO $DATA GROUP WAS FOUND

>>> CPU        TIME:   STEP =      0.90 ,  TOTAL =        1.3 SECONDS (    0.0 MIN)
>>> WALL CLOCK TIME:   STEP =      0.89 ,  TOTAL =        0.9 SECONDS (    0.0 MIN)
>>> CPU UTILIZATION:   STEP =    100.74%,  TOTAL =     145.51%

>>>           0 WORDS OF    DYNAMIC MEMORY USED
>>> EXECUTION OF FIREFLY TERMINATED ABNORMALLY AT 19:34:26 LT  20-JUN-2010
>>>
>>>
>>>
>>>
>>>
>>>On Sun Jun 20 '10 8:04pm, Miro Moman wrote
>>>------------------------------------------
>>>>Hello,

>>>>I am trying to run the MPICH2-Linux version of Firefly (firefly_71g_linux_mpich2_p4) in a local machine with two quad-core Nehalem processors. I have started the mpd daemon as per the MPICH website instructions.

>>>>This is the command line I am using:

>>>>/home/mirix/Downloads/firefly/firefly_71g_linux_mpich2_p4/firefly -i complex.inp -o output.out /disk/scratch/pcgamess /tmp/pcgamess -p4pg /home/mirix/Downloads/firefly/combo/procgrp

>>>>The input file is the example from Combo (optimization of the final complex).

>>>>As for the procgrp file I have tried:

>>>>local 7 and aeolus 7 /home/mirix/Downloads/firefly/firefly_71g_linux_mpich2_p4/firefly

>>>>Firefly correctly detects 8 cores and 16 threads but it only uses one processor.

>>>>Best regards,

>>>>Miro

[ This message was edited on Mon Jun 21 '10 at 3:06pm by the author ]