This is more of an announcement or warning than a proper blog post:
Both FX8350 and FX8150 have trouble running the pspw module causing the calculation to lead to exploding structures:
http://www.nwchem-sw.org/index.php/Special:AWCforum/st/id1059/Issue_with_pspw_using_nwchem_6.3....html
My other nodes have no trouble running the job in question. Also, the issue was only found in nwchem 6.3 -- nwchem 6.1.1 worked fine. So it's not an FX83x50 related fault per se.
Again, see the post at the nwchem-sw.org site for more information.
Lindqvist - a blog about Linux and Science. Mostly.
Showing posts with label pspw. Show all posts
Showing posts with label pspw. Show all posts
25 November 2013
24 May 2012
162. PSPW/Carr-Parrinello using ECCE
This is more of a note to self about carr-parrinello using ecce/nwchem. As always, this isn't about the science, but about making the computation run at all. And what I may consider a bug may in fact be a feature.
If you simply click your way through ecce and try to launch a pspw carr-parrinello calc, it will fail.
Two problems:
Problem number one comes down to this:
"Velocity Wavefunction Datafile
The one-electron orbital velocities are stored in a velocity wavefunction datafile. This is a binary file and cannot be directly edited. This datafile is used by the Car-Parrinello task and can be generated using the v_wavefunction_initializer task."
The dependence on certain files (at a minimum, .movecs) being present and the need for optimisation before CPMD and the fact that either
task pspw energy
or
task pspw optimize
will more often than not prevent your ecce.out file from showing any of the MD stuff means it's still better to set up your file by hand and run everything by hand in a dedicated directory. Ecce doesn't copy runtime file back and forth, and that's the main problem here.
Really, what I find a problem is that I'd like to optimize and equilibriate a set of molecules, then continue using the equilibriated set.
If all you're trying to do is to get something, anything to work to get a feel for how this stuff works, then continue reading.
Problematic example file:
Quick 'solution'
The line numbers are added by me. Remove them before running.
You can also stick task pspw energy or optimize in there -- but the way ecce does it, with just a task pspw carr-parrinello, won't work. Either way, it'd be nice to be able to carry over the movecs files between calculations.
See below for various errors:
Error #1:
If you set up the run using ecce, it won't work and there won't be any real error message to explain why the run exits immediately.
If you could run all your job in the same directory that wouldn't be a problem.
Error #2
We chucked task pspw steepest_descent in before our task pspw carr-parrinello and now get a new error: out of heap memory. Easily fixed. You can set e.g. 200MW under pspw/details or add
memory 200 MW
by hand.
Of course, if you add it by clicking in ecce then your task pspw steepest_descent line will be removed, so you'll have to add that by hand again.
Error #3
According to the manual "This [movecs] datafile is used by the Car-Parrinello task and can be generated using the v_wavefunction_initializer task."
Well, try
task v_wavefunction_initialize
and you get
Error 4
Going full out:
Error 5:
If you simply click your way through ecce and try to launch a pspw carr-parrinello calc, it will fail.
Two problems:
- task pspw carr-parrinello expects a .movecs file to be present. You can 'solve' this by putting task pspw steepest_descent before you task pspw carr-parrinello statement
- if you relaunch a run, often you get a crash with an error referring to writing after EOF. You can solve this by cleaning out your run directory.
Problem number one comes down to this:
"Velocity Wavefunction Datafile
The one-electron orbital velocities are stored in a velocity wavefunction datafile. This is a binary file and cannot be directly edited. This datafile is used by the Car-Parrinello task and can be generated using the v_wavefunction_initializer task."
The dependence on certain files (at a minimum, .movecs) being present and the need for optimisation before CPMD and the fact that either
task pspw energy
or
task pspw optimize
will more often than not prevent your ecce.out file from showing any of the MD stuff means it's still better to set up your file by hand and run everything by hand in a dedicated directory. Ecce doesn't copy runtime file back and forth, and that's the main problem here.
Really, what I find a problem is that I'd like to optimize and equilibriate a set of molecules, then continue using the equilibriated set.
If all you're trying to do is to get something, anything to work to get a feel for how this stuff works, then continue reading.
Problematic example file:
1 scratch_dir /home/me/jobs/scratch
2 Title "biphenyl_ground_twisted_cpmd_1-1"
3
4 Start biphenyl_ground_twisted_cpmd_1-1
5
6 echo
7
8 charge 0
9
10 geometry autosym units angstrom
11 C 0.00676622 3.53807 0.0197363
12 C -1.29633 2.88855 0.554869
13 C -1.31879 1.38415 0.519460
14 C 0.00129627 0.730174 -0.000557722
15 C 1.28746 1.38368 -0.578129
16 C 1.31931 2.90453 -0.512952
17 C -0.0100394 -0.758319 -0.0224661
18 C 1.33004 -1.36336 0.563945
19 C 1.24425 -2.89848 0.485842
20 C -1.31683 -1.36948 -0.531559
21 C 0.0254501 -3.54181 0.0318405
22 C -1.30632 -2.89413 -0.540694
23 H 0.0916004 4.71976 0.273191
24 H -2.74374 3.75562 1.47791
25 H -2.78549 0.594633 1.40665
26 H 2.70470 3.74589 -1.20122
27 H 3.09496 -3.77313 1.52949
28 H -2.76973 -0.640827 -1.49262
29 H 0.0203915 -4.70472 -0.288098
30 H -2.76848 -3.72979 -1.38695
31 H 2.88815 -0.631319 1.39550
32 H 2.66933 0.621436 -1.58686
33 end
34
35 ecce_print ecce.out
36
37 nwpw
38 mult 1
39 np_dimensions -1 -1
40 tolerances 1e-7 1e-7
41 car-parrinello
42 time_step 5.000000e+00
43 fake_mass 5.000000e+02
44 loop 10 100
45 scaling 1.000000e+00 1.000000e+00
46 end
47 end
48
49 task pspw car-parrinello
Quick 'solution'
3 memory 200mw
48 task pspw steepest_descent
The line numbers are added by me. Remove them before running.
You can also stick task pspw energy or optimize in there -- but the way ecce does it, with just a task pspw carr-parrinello, won't work. Either way, it'd be nice to be able to carry over the movecs files between calculations.
See below for various errors:
Error #1:
If you set up the run using ecce, it won't work and there won't be any real error message to explain why the run exits immediately.
294 >>> JOB STARTED AT Thu May 24 14:19:04 2012 <<<
295 ================ input data ========================
296 library name resolved from: compiled reference
297 NWCHEM_NWPW_LIBRARY set to: </opt/nwchem/nwchem-6.1/src/nwpw/libraryps/>
298 library name resolved from: compiled reference
299 NWCHEM_NWPW_LIBRARY set to: </opt/nwchem/nwchem-6.1/src/nwpw/libraryps/>
300
301 -----ECCE Log Information-----
302 Starting Job: Thu May 24 14:19:02 EST 2012
303 Using /home/me/jobs/scratch as nwchem SCRATCH_DIR
304 nwchem exit status = -1
305 Final exit status = -1
306 Completed Job: Thu May 24 14:19:05 EST 2012
If you launch the run in the terminal (without mpirun -- mpi suppresses error messages sometimes) you get:
>>> JOB STARTED AT Thu May 24 14:20:15 2012 <<<
================ input data ========================
library name resolved from: compiled reference
NWCHEM_NWPW_LIBRARY set to: </opt/nwchem/nwchem-6.1/src/nwpw/libraryps/>
library name resolved from: compiled reference
NWCHEM_NWPW_LIBRARY set to: </opt/nwchem/nwchem-6.1/src/nwpw/libraryps/>
ERROR: Could not open pipe from input file
The reason is that ecce doesn't carry files over from previous simulations -- you need the .movecs file. This can be generated by
task pspw steepest_descent
If you could run all your job in the same directory that wouldn't be a problem.
Error #2
438 >>> JOB STARTED AT Thu May 24 14:24:38 2012 <<<
439 ================ input data ========================
440 ------------------------------------------------------------------------
441 out of heap memory 0
442 ------------------------------------------------------------------------
443 ------------------------------------------------------------------------
444 current input line :
445 48: task pspw energy
446 ------------------------------------------------------------------------
447 ------------------------------------------------------------------------
448 ------------------------------------------------------------------------
449 For more information see the NWChem manual at http://www.nwchem-sw.org/ index.php/NWChem_Documentation
memory 200 MW
by hand.
Of course, if you add it by clicking in ecce then your task pspw steepest_descent line will be removed, so you'll have to add that by hand again.
Error #3
According to the manual "This [movecs] datafile is used by the Car-Parrinello task and can be generated using the v_wavefunction_initializer task."
Well, try
task v_wavefunction_initialize
and you get
>>>> PSPW Serial Module - v_wavefunction_initializer <<<<
0:Segmentation Violation error, status=: 11
(rank:0 hostname:beryllium pid:24675):ARMCI DASSERT fail. ../../ga-5-1/armci/src/common/signaltrap.c:SigSegvHandler():310 cond:0
Last System Error Message from Task 0:: No such file or directory
And you find that there's a file called ????
Error 4
Going full out:
task pspw wavefunction_initializer
task pspw pseudopotential_formatter
task pspw v_wavefunction_initializer
task pspw car-parrinello
gives
>>>> PSPW Serial Module - wavefunction_initializer <<<<
0:Floating Point Exception error, status=: 8
(rank:0 hostname:beryllium pid:26026):ARMCI DASSERT fail. ../../ga-5-1/armci/src/common/signaltrap.c:SigFpeHandler():249 cond:0
Last System Error Message from Task 0:: No such file or directory
Error 5:
If you haven't cleared out your run directory you get this via ecce
============ Car-Parrinello iteration ==============
>>> ITERATION STARTED AT Thu May 24 18:03:07 2012 <<<
iter. KE+Energy Energy KE_psi KE_ion Temperature
------------------------------------------------------------------------------------
10 -0.1662131203E+02 -0.1662582428E+02 0.43690E-02 0.39005E-02 143.80
-----ECCE Log Information-----
Starting Job: Thu May 24 18:00:41 EST 2012
and this if you run in the terminal
At line 847 of file cpmdv5.F (unit = 31, file = './cpmd_test.emotion')
Fortran runtime error: Sequential READ or WRITE not allowed after EOF marker, possibly use REWIND or BACKSPACE
10 0.1175850345E+06 0.3940717762E+03 0.18793E-03 0.27950E-02 1852.03
--------------------------------------------------------------------------
mpirun has exited due to process rank 0 with PID 26303 on
node beryllium exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
------------------------------------------------------------------------
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