Hi everyone,
I'm having trouble attaining frequencies after successful geometry optimization.
I encounter the error "no mirroring in shellfockbld" during the Hessian calculation.
There was a previous thread with a similar title and the solution was increasing the memory
allocated to NWChem - link to thread below.
http://nwchemgit.github.io/Special_AWCforum/st/id2187/frequencies%3A_no_mirroring_...
I have tried allocating more memory the same way and have not had any success.
Here is my input file:
start EDA_6_H2O_GP_OPT_xfine
title "EDA_6_H2O_GP_OPT_xfine"
memory 2048 mb
charge 0
geometry
C 1.496677260000 2.299274080000 -0.261005940000
C 2.251827930000 0.982643630000 -0.078659180000
N 0.466165580000 2.543218510000 0.782160470000
H 0.989190180000 2.278449540000 -1.227091070000
H 2.221140510000 3.121983400000 -0.293019740000
H -0.364840580000 2.929696630000 0.330215700000
H 0.798143870000 3.231032290000 1.450946180000
N 1.357712540000 -0.180055180000 -0.180528220000
H 2.806760920000 1.003841810000 0.871956320000
H 2.997230550000 0.914340540000 -0.876998740000
H 0.894773730000 -0.334550380000 0.711291380000
H 1.873995970000 -1.037628660000 -0.371871010000
O -0.633748990000 0.413524230000 2.157501800000
H -0.555530230000 0.559754080000 3.103950240000
H -0.244472440000 1.215088200000 1.690220320000
O -2.180486710000 -1.335774760000 0.771767960000
H -3.087384310000 -1.347071460000 1.092061280000
H -1.685454710000 -0.709585450000 1.351857750000
O -1.138125350000 0.100923950000 -1.577504050000
H -0.215903260000 -0.013466240000 -1.236562670000
H -1.675389930000 -0.416864000000 -0.958452580000
O 1.930578810000 -3.160966080000 -0.360364290000
H 0.978498070000 -3.378407690000 -0.300487570000
H 2.391646970000 -3.880023790000 0.079531100000
O -1.782094040000 2.726401600000 -1.134076410000
H -1.613707030000 1.786281310000 -1.381601130000
H -2.111973370000 3.157903010000 -1.926412650000
O -0.839940410000 -3.596016020000 -0.267669660000
H -1.182645370000 -3.624257740000 -1.166616660000
H -1.316786590000 -2.860566530000 0.163942950000
end
basis
* library 6-311++G**
bqH library H 6-311++G**
bqC library C 6-311++G**
bqN library N 6-311++G**
bqO library O 6-311++G**
end
dft
tolerances tight
grid xfine nodisk
xc b3lyp
direct
iterations 500
end
driver
tight
maxiter 500
end
set int:txs:limxmem 1000000000
task dft optimize
task dft freq
And the relevant output (after geometry optimization)
center of mass
--------------
x = -0.01464156 y = -0.02790693 z = -0.01046310
moments of inertia (a.u.)
------------------
3246.887169866180 4.407034716602 1.313138832365
4.407034716602 2078.859572803626 13.106922698178
1.313138832365 13.106922698178 4020.478918167987
Multipole analysis of the density
---------------------------------
L x y z total alpha beta nuclear
- - - - ----- ----- ---- -------
0 0 0 0 -0.000000 -47.000000 -47.000000 94.000000
1 1 0 0 -0.242336 -0.108823 -0.108823 -0.024691
1 0 1 0 0.797674 0.093561 0.093561 0.610551
1 0 0 1 1.355258 0.446935 0.446935 0.461387
2 2 0 0 -52.007714 -431.057305 -431.057305 810.106896
2 1 1 0 7.632105 -2.021271 -2.021271 11.674647
2 1 0 1 -2.153425 1.103431 1.103431 -4.360286
2 0 2 0 -41.108726 -757.942978 -757.942978 1474.777229
2 0 1 1 -5.809795 3.858838 3.858838 -13.527471
2 0 0 2 -44.716788 -213.121157 -213.121157 381.525525
HESSIAN: the one electron contributions are done in 54.7s
no mirroring in shellfockbld
HESSIAN: 2-el 1st deriv. term done in 158.6s
HESSIAN: 2-el 2nd deriv. term done in 36.1s
stpr_wrt_fd_from_sq: overwrite of existing file:./EDA_6_H2O_GP_OPT.hess
stpr_wrt_fd_dipole: overwrite of existing file./EDA_6_H2O_GP_OPT.fd_ddipole
HESSIAN: the two electron contributions are done in 1679.8s
no mirroring in shellfockbld
PE 0 [Wed Feb 1 18:02:22 2017] [c5-0c0s1n1] [nid00965] LIBDMAPP ERROR: Unsuccessful memory registration.
PE 11 [Wed Feb 1 18:02:22 2017] [c5-0c0s1n1] [nid00965] LIBDMAPP ERROR: Unsuccessful memory registration.
PE 7 [Wed Feb 1 18:02:22 2017] [c5-0c0s1n1] [nid00965] LIBDMAPP ERROR: Unsuccessful memory registration.
PE 9 [Wed Feb 1 18:02:22 2017] [c5-0c0s1n1] [nid00965] LIBDMAPP ERROR: Unsuccessful memory registration.
PE 7 - Current Buddyinfo stats: Small blocks free pagecount 444485, free bytes 1820610560
PE 7 - Current Buddyinfo stats: Huge blocks free pagecount 1408, free bytes 11811160064
PE 7 - Initial Buddyinfo stats: Small blocks free pagecount 462404, free bytes 1894006784
PE 7 - Initial Buddyinfo stats: Huge blocks free pagecount 6697, free bytes 56178507776
PE 9 - Current Buddyinfo stats: Small blocks free pagecount 444485, free bytes 1820610560
PE 9 - Current Buddyinfo stats: Huge blocks free pagecount 1408, free bytes 11811160064
PE 9 - Initial Buddyinfo stats: Small blocks free pagecount 462404, free bytes 1894006784
PE 9 - Initial Buddyinfo stats: Huge blocks free pagecount 6697, free bytes 56178507776
PE 11 - Current Buddyinfo stats: Small blocks free pagecount 444454, free bytes 1820483584
PE 11 - Current Buddyinfo stats: Huge blocks free pagecount 1408, free bytes 11811160064
PE 11 - Initial Buddyinfo stats: Small blocks free pagecount 462404, free bytes 1894006784
PE 11 - Initial Buddyinfo stats: Huge blocks free pagecount 6697, free bytes 56178507776
nwchem: ../../ga-5-3/comex/src-dmapp/comex.c:890: _comex_malloc_local: Assertion `status == DMAPP_RC_SUCCESS' failed.
nwchem: ../../ga-5-3/comex/src-dmapp/comex.c:890: _comex_malloc_local: Assertion `status == DMAPP_RC_SUCCESS' failed.
nwchem: ../../ga-5-3/comex/src-dmapp/comex.c:890: _comex_malloc_local: Assertion `status == DMAPP_RC_SUCCESS' failed.
forrtl: error (76): Abort trap signal
Image PC Routine Line Source
libintlc.so.5 00002AAAAB183229 Unknown Unknown Unknown
libintlc.so.5 00002AAAAB181BA0 Unknown Unknown Unknown
nwchem 00000000036F8172 Unknown Unknown Unknown
nwchem 00000000036A0263 Unknown Unknown Unknown
nwchem 00000000036A6912 Unknown Unknown Unknown
libpthread.so.0 00002AAAABFA5850 Unknown Unknown Unknown
libc.so.6 00002AAAAC45E875 Unknown Unknown Unknown
libc.so.6 00002AAAAC45FE51 Unknown Unknown Unknown
libc.so.6 00002AAAAC457740 Unknown Unknown Unknown
nwchem 000000000358E4A9 Unknown Unknown Unknown
nwchem 000000000355FA4F Unknown Unknown Unknown
nwchem 000000000355EADA Unknown Unknown Unknown
nwchem 00000000035633E2 Unknown Unknown Unknown
nwchem 00000000033E694D Unknown Unknown Unknown
nwchem 00000000009C569C Unknown Unknown Unknown
nwchem 0000000000A1FF37 Unknown Unknown Unknown
nwchem 0000000000AED3A4 Unknown Unknown Unknown
forrtl: error (76): Abort trap signal
Image PC Routine Line Source
libintlc.so.5 00002AAAAB183229 Unknown Unknown Unknown
libintlc.so.5 00002AAAAB181BA0 Unknown Unknown Unknown
nwchem 00000000036F8172 Unknown Unknown Unknown
nwchem 00000000036A0263 Unknown Unknown Unknown
nwchem 00000000036A6912 Unknown Unknown Unknown
libpthread.so.0 00002AAAABFA5850 Unknown Unknown Unknown
libc.so.6 00002AAAAC45E875 Unknown Unknown Unknown
libc.so.6 00002AAAAC45FE51 Unknown Unknown Unknown
libc.so.6 00002AAAAC457740 Unknown Unknown Unknown
nwchem 000000000358E4A9 Unknown Unknown Unknown
nwchem 000000000355FA4F Unknown Unknown Unknown
nwchem 000000000355EADA Unknown Unknown Unknown
nwchem 00000000035633E2 Unknown Unknown Unknown
nwchem 00000000033E694D Unknown Unknown Unknown
nwchem 00000000009C569C Unknown Unknown Unknown
nwchem 0000000000A1FF37 Unknown Unknown Unknown
nwchem 0000000000AED3A4 Unknown Unknown Unknown
forrtl: error (76): Abort trap signal
Image PC Routine Line Source
libintlc.so.5 00002AAAAB183229 Unknown Unknown Unknown
libintlc.so.5 00002AAAAB181BA0 Unknown Unknown Unknown
nwchem 00000000036F8172 Unknown Unknown Unknown
nwchem 00000000036A0263 Unknown Unknown Unknown
nwchem 00000000036A6912 Unknown Unknown Unknown
libpthread.so.0 00002AAAABFA5850 Unknown Unknown Unknown
libc.so.6 00002AAAAC45E875 Unknown Unknown Unknown
libc.so.6 00002AAAAC45FE51 Unknown Unknown Unknown
libc.so.6 00002AAAAC457740 Unknown Unknown Unknown
nwchem 000000000358E4A9 Unknown Unknown Unknown
nwchem 000000000355FA4F Unknown Unknown Unknown
nwchem 000000000355EADA Unknown Unknown Unknown
nwchem 00000000035633E2 Unknown Unknown Unknown
nwchem 00000000033E694D Unknown Unknown Unknown
nwchem 00000000009C569C Unknown Unknown Unknown
nwchem 0000000000A1FF37 Unknown Unknown Unknown
nwchem 0000000000AED3A4 Unknown Unknown Unknown
PE 0 - Current Buddyinfo stats: Small blocks free pagecount 446675, free bytes 1829580800
PE 0 - Current Buddyinfo stats: Huge blocks free pagecount 1813, free bytes 15208546304
PE 0 - Initial Buddyinfo stats: Small blocks free pagecount 462404, free bytes 1894006784
PE 0 - Initial Buddyinfo stats: Huge blocks free pagecount 6697, free bytes 56178507776
nwchem: ../../ga-5-3/comex/src-dmapp/comex.c:890: _comex_malloc_local: Assertion `status == DMAPP_RC_SUCCESS' failed.
forrtl: error (76): Abort trap signal
Image PC Routine Line Source
libintlc.so.5 00002AAAAB183229 Unknown Unknown Unknown
libintlc.so.5 00002AAAAB181BA0 Unknown Unknown Unknown
nwchem 00000000036F8172 Unknown Unknown Unknown
nwchem 00000000036A0263 Unknown Unknown Unknown
nwchem 00000000036A6912 Unknown Unknown Unknown
libpthread.so.0 00002AAAABFA5850 Unknown Unknown Unknown
libc.so.6 00002AAAAC45E875 Unknown Unknown Unknown
libc.so.6 00002AAAAC45FE51 Unknown Unknown Unknown
libc.so.6 00002AAAAC457740 Unknown Unknown Unknown
nwchem 000000000358E4A9 Unknown Unknown Unknown
nwchem 000000000355FA4F Unknown Unknown Unknown
nwchem 000000000355EADA Unknown Unknown Unknown
nwchem 00000000035633E2 Unknown Unknown Unknown
nwchem 00000000033E694D Unknown Unknown Unknown
nwchem 00000000009C569C Unknown Unknown Unknown
nwchem 0000000000A1FF37 Unknown Unknown Unknown
nwchem 0000000000AED3A4 Unknown Unknown Unknown
_pmiu_daemon(SIGCHLD): [NID 00965] [c5-0c0s1n1] [Wed Feb 1 18:02:22 2017] PE RANK 11 exit signal Aborted
[NID 00965] 2017-02-01 18:02:49 Apid 6936814: initiated application termination
Application 6936814 exit codes: 134
Application 6936814 resources: utime ~4791s, stime ~21s, Rss ~251228, inblocks ~407584, outblocks ~492764
I did some digging through the source code to find where this specific error is generated and seems to
originate from line 397 in"shell_fock_build.F" which is dependent on the following if statement
if(ga_nodeid().eq.0) then
write(6,*) ' no mirroring in shellfockbld'
call util_flush(6)
endif
I recognized ga_nodeid() from the manual in the section for Python extensions, pg 440 of NWChem 6.5 Documentation.
ga_nodeid() -- returns the number of the parallel process
And when I tried to run the following example input described on the same page:
python
print 'Hello world from process ', ga_nodeid()
end
task python
I encountered the following error:
------------------------------------------------------------------------
python_input is not in this build of NWChem 0
------------------------------------------------------------------------
------------------------------------------------------------------------
current input line :
200: python
------------------------------------------------------------------------
------------------------------------------------------------------------
A feature requested has not yet been implemented
Received an Error in Communication
Rank 0 [Fri Jun 2 16:00:51 2017] [c7-0c1s1n1] application called MPI_Abort(comm=0x84000004, -1) - process 0
------------------------------------------------------------------------
For more information see the NWChem manual at
http://nwchemgit.github.io/index.php/NWChem_Documentation
For further details see manual section:
forrtl: error (76): Abort trap signal
Image PC Routine Line Source
libintlc.so.5 00002AAAAB184229 Unknown Unknown Unknown
libintlc.so.5 00002AAAAB182BA0 Unknown Unknown Unknown
nwchem 00000000036F8172 Unknown Unknown Unknown
nwchem 00000000036A0263 Unknown Unknown Unknown
nwchem 00000000036A6912 Unknown Unknown Unknown
libpthread.so.0 00002AAAABFA5850 Unknown Unknown Unknown
libc.so.6 00002AAAAC45F875 Unknown Unknown Unknown
libc.so.6 00002AAAAC460E51 Unknown Unknown Unknown
libmpich_intel.so 00002AAAAB4A16A6 Unknown Unknown Unknown
libmpich_intel.so 00002AAAAB58C063 Unknown Unknown Unknown
nwchem 0000000003452333 Unknown Unknown Unknown
nwchem 00000000033EBF37 Unknown Unknown Unknown
nwchem 0000000000C4033A Unknown Unknown Unknown
nwchem 0000000000410EFF Unknown Unknown Unknown
nwchem 000000000040D922 Unknown Unknown Unknown
nwchem 000000000040D456 Unknown Unknown Unknown
libc.so.6 00002AAAAC44BC36 Unknown Unknown Unknown
nwchem 000000000040D349 Unknown Unknown Unknown
_pmiu_daemon(SIGCHLD): [NID 01413] [c7-0c1s1n1] [Fri Jun 2 16:00:51 2017] PE RANK 0 exit signal Aborted
[NID 01413] 2017-06-02 16:02:48 Apid 7608674: initiated application termination
Application 7608674 exit codes: 134
Application 7608674 exit signals: Killed
Application 7608674 resources: utime ~3s, stime ~3s, Rss ~247736, inblocks ~395664, outblocks ~540259
I'm running NWChem 6.5, revision 26243, ga revision 105063, 24 processors per node, 64 GB shared RAM, Cray XC40 Supercomputer.
Hoping there's a simple solution to this.
Thanks.
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