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#1 2025-02-20 07:45:53
- RE_DRC
- Member
- Registered: 2025-02-12
- Posts: 3
Problem in run QM/MM with GROMACS
Dear all,
After compiling GROMACS and OpenMolcas, I started testing using the 834.input file. Now I'm encountering the following issue: Could this be due to incorrect compilation of the software, or is there another environmental problem? My OpenMolcas version is 24.10, and GROMACS is the QMMM branch, approximately version 5.0.x.
Thank you very much for your help!
Re_drc
This run of MOLCAS is using the pymolcas driver
OPE
OPE NMOL CASOP ENMOLC A SO
OPE NMOLC AS OP EN MO LC AS OP
OPENM OL CA SO PE NM OL CA SOP EN
OP EN MO LC AS OP ENMOL CASO PENMOL
OP EN MO LC AS OP EN MO LC ASO
OP E NMOL C AS OP EN MO LC AS OP
OP E NMO LC AS OPEN MO LCASOP EN M
O PEN MO LCA SO
OPE NMO L CAS OP
OPENMOL CASOP ENMOL CASOPE
OPENMOLCA SOPENMOLCASOPEN MOLCASOPE
OPENMOLCAS OP EN MOL CAS
OPENMOLCAS OP ENM O LCA
OPENMOLCAS OPEN MOLCASO P E NMO
OPENMOLCAS OP E N MOL
OPENMOLCA SO PENM O L CAS OPEN MO LCAS
OPENMOLCA SOP ENM O L CAS OP EN MOLC AS O
OPENMOLCA SOPE NM O LCA S OP EN MO
OPENMOLC AS O PEN M OL CA SOPE
OPENMO LCASOPE NMOL C ASO P ENMOLC AS
OPE NMO LCA SO P E NM OL CA SO PE N MO
OPENMOLCA SOPE NMO LCAS O P ENMO
OPENMOLCASOPENMOLCASOPENMOLCASOPENMOLCA
OPENMOLCASOPENMOLCASOPENMOLCASOPE
OPENMOLCASOPENMOLCASOPENM
OPENMOLCASOPENMOLCA version: v24.10 ?
OPENMOLCASO
OPE tag:
OpenMolcas is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License version 2.1.
OpenMolcas is distributed in the hope that it will be useful, but it
is provided "as is" and without any express or implied warranties.
For more details see the full text of the license in the file
LICENSE or in <http://www.gnu.org/licenses/>.
Copyright (C) The OpenMolcas Authors
For the author list and the recommended citation,
consult the file CONTRIBUTORS.md
*************************************************
* pymolcas version py2.29 *
* build c0481229b6f3f65ed2c83878be511d3d *
* (after the EMIL interpreter by V. Veryazov) *
*************************************************
configuration info
------------------
Host name: master (Linux)
C Compiler ID: GNU
C flags: -std=gnu99 -fopenmp
Fortran Compiler ID: GNU
Fortran flags: -fno-aggressive-loop-optimizations -cpp -fdefault-integer-8 -fopenmp
Definitions: _MOLCAS_;_I8_;_LINUX_
Parallel: OFF (GA=OFF)
----------------------------------------------------------------------------
|
| Project: 834
| Submitted from: /home/yinbw-hgy
| Scratch area: /home/yinbw-hgy/tmp/834
| Save outputs to: /home/yinbw-hgy
| Molcas: /home/yinbw-hgy/software/openmolcas2410_gmx
|
| Scratch area is NOT empty
|
| MOLCAS_DRIVER = /home/yinbw-hgy/software/openmolcas2410_gmx/bin/pymolcas
| MOLCAS_NPROCS = 1
| MOLCAS_PRINT = 3
| MOLCAS_SOURCE = /home/yinbw-hgy/software/openmolcas2410_gmx
| MOLCAS_STRUCTURE = 0
|
----------------------------------------------------------------------------
++ --------- Input file ---------
>>> RM -FORCE TEST_GROMACS
>>> IF ($MOLCAS_DRIVER == UNKNOWN_VARIABLE)
>>> EXPORT MOLCAS_DRIVER = molcas
>>> END IF
>>> SHELL $MOLCAS_DRIVER have_feature gromacs || touch TEST_GROMACS
>>> IF (-FILE TEST_GROMACS)
>>> EXIT 36
>>> END IF
>>> SHELL grompp_d -n index
>>> EXPORT GMX_NB_GENERIC = 1
>>> EXPORT GMX_MAXBACKUP = -1
&GATEWAY
Gromacs
Simple
Basis
cc-pVDZ
Group
NoSym
NoCD
>>> DO WHILE
&SEWARD
&ESPF
External
Gromacs
MMIterations
1000
&SCF
&SLAPAF
Cartesian
>>> END DO
-- ----------------------------------
>>> RM -FORCE TEST_GROMACS
>>> IF ($MOLCAS_DRIVER == UNKNOWN_VARIABLE)
(Skipped)
>>> SHELL /home/yinbw-hgy/software/openmolcas2410_gmx/bin/pymolcas have_feature gromacs || touch TEST_GROMACS
>>> IF (-FILE TEST_GROMACS)
(Skipped)
>>> SHELL grompp_d -n index
GROMACS: gmx grompp, VERSION 5.1-dev (double precision)
GROMACS is written by:
Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch
Gerrit Groenhof Christoph Junghans Peter Kasson Carsten Kutzner
Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff
Erik Marklund Teemu Murtola Szilard Pall Sander Pronk
Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
Peter Tieleman Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2014, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx grompp, VERSION 5.1-dev (double precision)
Executable: /home/yinbw-hgy/software/gmx_qmmm/bin/gmx_d
Library dir: /home/yinbw-hgy/software/gmx_qmmm/share/gromacs/top
Command line:
grompp_d -n index
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.12#
NOTE 1 [file grompp.mdp]:
The group cutoff scheme is deprecated in Gromacs 5.0 and will be removed
in a future release when all interaction forms are supported for the
verlet scheme. The verlet scheme already scales better, and it is
compatible with GPUs and other accelerators.
NOTE 2 [file grompp.mdp]:
For a correct single-point energy evaluation with nsteps = 0, use
continuation = yes to avoid constraining the input coordinates.
NOTE 3 [file grompp.mdp]:
Simulating without cut-offs can be (slightly) faster with nstlist=0,
nstype=simple and only one MPI rank
NOTE 4 [file grompp.mdp]:
Tumbling and or flying ice-cubes: We are not removing rotation around
center of mass in a non-periodic system. You should probably set
comm_mode = ANGULAR.
Setting the LD random seed to 3298690897
Generated 331705 of the 331705 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 331705 of the 331705 1-4 parameter combinations
Excluding 2 bonded neighbours molecule type 'SOLQM'
Excluding 2 bonded neighbours molecule type 'SOL'
Number of degrees of freedom in T-Coupling group rest is 15.00
nr. of CONNBONDS present already: 2
There were 4 notes
Back Off! I just backed up topol.tpr to ./#topol.tpr.12#
gcq#189: "It's So Fast It's Slow" (F. Black)
This run will generate roughly 0 Mb of data
>>> EXPORT GMX_NB_GENERIC = 1
>>> EXPORT GMX_MAXBACKUP = -1
--- Start Module: gateway at Thu Feb 20 13:15:15 2025 ---
()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()
&GATEWAY
only a single process is used
available to each process: 16 GB of memory, 1 thread
pid: 93005
()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()()
Reading file topol.tpr, VERSION 5.1-dev (double precision)
Reading file topol.tpr, VERSION 5.1-dev (double precision)
Program received signal SIGABRT: Process abort signal.
Backtrace for this error:
--- Stop Module: gateway at Thu Feb 20 13:15:15 2025 /rc=-13 ---
*** files: xmldump
saved to directory /home/yinbw-hgy
.########################.
.# Non-zero return code #.
.########################.
Timing: Wall=0.06 User=0.03 System=0.03*** Error in `/home/yinbw-hgy/software/openmolcas2410_gmx/bin/gateway.exe': free(): invalid pointer: 0x000000000bbc73 10 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x81329)[0x2af6c09ef329]
/home/yinbw-hgy/software/gmx_qmmm/lib64/libgromacs_d.so.1(gmx_fio_close+0x11f)[0x2af6beccea6f]
/home/yinbw-hgy/software/gmx_qmmm/lib64/libgromacs_d.so.1(read_tpx+0x6a)[0x2af6bed039ba]
/home/yinbw-hgy/software/gmx_qmmm/lib64/libgromacs_d.so.1(_ZN3gmx7MMSlave7readTprEPKcP8_IO_FILE+0xda)[0x2af6bec8525a]
/home/yinbw-hgy/software/gmx_qmmm/lib64/libgromacs_d.so.1(mmslave_read_tpr+0x15)[0x2af6bec853b5]
/home/yinbw-hgy/software/openmolcas2410_gmx/bin/gateway.exe[0x484fad]
/home/yinbw-hgy/software/openmolcas2410_gmx/bin/gateway.exe[0x41af09]
/home/yinbw-hgy/software/openmolcas2410_gmx/bin/gateway.exe[0x4053c5]
/home/yinbw-hgy/software/openmolcas2410_gmx/bin/gateway.exe[0x405165]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x2af6c0990555]
/home/yinbw-hgy/software/openmolcas2410_gmx/bin/gateway.exe[0x4051a1]
======= Memory map: ========
00400000-00569000 r-xp 00000000 08:11 35151177310 /home/yinbw-hgy/software/openmolcas2410_gmx/ bin/gateway.exe
00768000-00769000 r--p 00168000 08:11 35151177310 /home/yinbw-hgy/software/openmolcas2410_gmx/ bin/gateway.exe
00769000-0237c000 rw-p 00169000 08:11 35151177310 /home/yinbw-hgy/software/openmolcas2410_gmx/ bin/gateway.exe
0237c000-0b08d000 rw-p 00000000 00:00 0
0bbc4000-0bc0f000 rw-p 00000000 00:00 0 [heap]
2af6b7f3f000-2af6b7f61000 r-xp 00000000 08:03 272045239 /usr/lib64/ld-2.17.so
2af6b7f61000-2af6b7f63000 rw-p 00000000 00:00 0
2af6b7f90000-2af6b80d3000 rw-p 00000000 00:00 0
2af6b8160000-2af6b8161000 r--p 00021000 08:03 272045239 /usr/lib64/ld-2.17.so
2af6b8161000-2af6b8162000 rw-p 00022000 08:03 272045239 /usr/lib64/ld-2.17.so
2af6b8162000-2af6b8163000 rw-p 00000000 00:00 0
2af6b8163000-2af6b83fd000 r-xp 00000000 08:03 272903697 /usr/lib64/libhdf5.so.8.0.1
2af6b83fd000-2af6b85fc000 ---p 0029a000 08:03 272903697 /usr/lib64/libhdf5.so.8.0.1
2af6b85fc000-2af6b8601000 r--p 00299000 08:03 272903697 /usr/lib64/libhdf5.so.8.0.1
2af6b8601000-2af6b8608000 rw-p 0029e000 08:03 272903697 /usr/lib64/libhdf5.so.8.0.1
2af6b8608000-2af6b8609000 rw-p 00000000 00:00 0
2af6b8609000-2af6b8e4d000 r-xp 00000000 08:03 539713629 /opt/intel2019/compilers_and_libraries_2019. 0.117/linux/mkl/lib/intel64_lin/libmkl_gf_ilp64.so
2af6b8e4d000-2af6b904d000 ---p 00844000 08:03 539713629 /opt/intel2019/compilers_and_libraries_2019. 0.117/linux/mkl/lib/intel64_lin/libmkl_gf_ilp64.so
2af6b904d000-2af6b904e000 r--p 00844000 08:03 539713629 /opt/intel2019/compilers_and_libraries_2019. 0.117/linux/mkl/lib/intel64_lin/libmkl_gf_ilp64.so
2af6b904e000-2af6b9060000 rw-p 00845000 08:03 539713629 /opt/intel2019/compilers_and_libraries_2019. 0.117/linux/mkl/lib/intel64_lin/libmkl_gf_ilp64.so
2af6b9060000-2af6b9066000 rw-p 00000000 00:00 0
2af6b9066000-2af6bcf2b000 r-xp 00000000 08:03 539479604 /opt/intel2019/compilers_and_libraries_2019. 0.117/linux/mkl/lib/intel64_lin/libmkl_core.so
2af6bcf2b000-2af6bd12b000 ---p 03ec5000 08:03 539479604 /opt/intel2019/compilers_and_libraries_2019. 0.117/linux/mkl/lib/intel64_lin/libmkl_core.so
2af6bd12b000-2af6bd132000 r--p 03ec5000 08:03 539479604 /opt/intel2019/compilers_and_libraries_2019. 0.117/linux/mkl/lib/intel64_lin/libmkl_core.so
2af6bd132000-2af6bd160000 rw-p 03ecc000 08:03 539479604 /opt/intel2019/compilers_and_libraries_2019. 0.117/linux/mkl/lib/intel64_lin/libmkl_core.so
2af6bd160000-2af6bd19f000 rw-p 00000000 00:00 0
2af6bd19f000-2af6be7bd000 r-xp 00000000 08:03 539713556 /opt/intel2019/compilers_and_libraries_2019. 0.117/linux/mkl/lib/intel64_lin/libmkl_gnu_thread.so
2af6be7bd000-2af6be9bc000 ---p 0161e000 08:03 539713556 /opt/intel2019/compilers_and_libraries_2019. 0.117/linux/mkl/lib/intel64_lin/libmkl_gnu_thread.so
2af6be9bc000-2af6be9c0000 r--p 0161d000 08:03 539713556 /opt/intel2019/compilers_and_libraries_2019. 0.117/linux/mkl/lib/intel64_lin/libmkl_gnu_thread.so
2af6be9c0000-2af6be9d8000 rw-p 01621000 08:03 539713556 /opt/intel2019/compilers_and_libraries_2019. 0.117/linux/mkl/lib/intel64_lin/libmkl_gnu_thread.so
2af6be9d8000-2af6bf877000 r-xp 00000000 08:11 54826571805 /home/yinbw-hgy/software/gmx_qmmm/lib64/libg romacs_d.so.1.0.0
2af6bf877000-2af6bfa76000 ---p 00e9f000 08:11 54826571805 /home/yinbw-hgy/software/gmx_qmmm/lib64/libg romacs_d.so.1.0.0
2af6bfa76000-2af6bfa85000 r--p 00e9e000 08:11 54826571805 /home/yinbw-hgy/software/gmx_qmmm/lib64/libg romacs_d.so.1.0.0
2af6bfa85000-2af6bfaa8000 rw-p 00ead000 08:11 54826571805 /home/yinbw-hgy/software/gmx_qmmm/lib64/libg romacs_d.so.1.0.0
2af6bfaa8000-2af6bfab5000 rw-p 00000000 00:00 0
2af6bfab5000-2af6bfbd4000 r-xp 00000000 08:03 268869255 /usr/lib64/libgfortran.so.3.0.0
2af6bfbd4000-2af6bfdd4000 ---p 0011f000 08:03 268869255 /usr/lib64/libgfortran.so.3.0.0
2af6bfdd4000-2af6bfdd5000 r--p 0011f000 08:03 268869255 /usr/lib64/libgfortran.so.3.0.0
2af6bfdd5000-2af6bfdd7000 rw-p 00120000 08:03 268869255 /usr/lib64/libgfortran.so.3.0.0
2af6bfdd7000-2af6bfed8000 r-xp 00000000 08:03 268456707 /usr/lib64/libm-2.17.so
2af6bfed8000-2af6c00d7000 ---p 00101000 08:03 268456707 /usr/lib64/libm-2.17.so
2af6c00d7000-2af6c00d8000 r--p 00100000 08:03 268456707 /usr/lib64/libm-2.17.so
2af6c00d8000-2af6c00d9000 rw-p 00101000 08:03 268456707 /usr/lib64/libm-2.17.so
2af6c00d9000-2af6c00fe000 r-xp 00000000 08:03 268525118 /usr/lib64/libgomp.so.1.0.0
2af6c00fe000-2af6c02fd000 ---p 00025000 08:03 268525118 /usr/lib64/libgomp.so.1.0.0
2af6c02fd000-2af6c02fe000 r--p 00024000 08:03 268525118 /usr/lib64/libgomp.so.1.0.0
2af6c02fe000-2af6c02ff000 rw-p 00025000 08:03 268525118 /usr/lib64/libgomp.so.1.0.0
2af6c02ff000-2af6c0315000 r-xp 00000000 08:03 1208601134 /opt/intel2019/inspector_2019.0.0.569751/lib 64/libgcc_s.so.1
2af6c0315000-2af6c0515000 ---p 00016000 08:03 1208601134 /opt/intel2019/inspector_2019.0.0.569751/lib 64/libgcc_s.so.1
2af6c0515000-2af6c0516000 rw-p 00016000 08:03 1208601134 /opt/intel2019/inspector_2019.0.0.569751/lib 64/libgcc_s.so.1
2af6c0516000-2af6c0551000 r-xp 00000000 08:03 268600585 /usr/lib64/libquadmath.so.0.0.0
2af6c0551000-2af6c0750000 ---p 0003b000 08:03 268600585 /usr/lib64/libquadmath.so.0.0.0
2af6c0750000-2af6c0751000 r--p 0003a000 08:03 268600585 /usr/lib64/libquadmath.so.0.0.0
2af6c0751000-2af6c0752000 rw-p 0003b000 08:03 268600585 /usr/lib64/libquadmath.so.0.0.0
2af6c0752000-2af6c0769000 r-xp 00000000 08:03 270544421 /usr/lib64/libpthread-2.17.so
2af6c0769000-2af6c0968000 ---p 00017000 08:03 270544421 /usr/lib64/libpthread-2.17.so
2af6c0968000-2af6c0969000 r--p 00016000 08:03 270544421 /usr/lib64/libpthread-2.17.so
2af6c0969000-2af6c096a000 rw-p 00017000 08:03 270544421 /usr/lib64/libpthread-2.17.so
2af6c096a000-2af6c096e000 rw-p 00000000 00:00 0
2af6c096e000-2af6c0b32000 r-xp 00000000 08:03 272045246 /usr/lib64/libc-2.17.so
2af6c0b32000-2af6c0d31000 ---p 001c4000 08:03 272045246 /usr/lib64/libc-2.17.so
2af6c0d31000-2af6c0d35000 r--p 001c3000 08:03 272045246 /usr/lib64/libc-2.17.so
2af6c0d35000-2af6c0d37000 rw-p 001c7000 08:03 272045246 /usr/lib64/libc-2.17.so
2af6c0d37000-2af6c0d3c000 rw-p 00000000 00:00 0
2af6c0d3c000-2af6c0d3e000 r-xp 00000000 08:03 272888375 /usr/lib64/libsz.so.2.0.1
2af6c0d3e000-2af6c0f3d000 ---p 00002000 08:03 272888375 /usr/lib64/libsz.so.2.0.1
2af6c0f3d000-2af6c0f3e000 r--p 00001000 08:03 272888375 /usr/lib64/libsz.so.2.0.1
2af6c0f3e000-2af6c0f3f000 rw-p 00002000 08:03 272888375 /usr/lib64/libsz.so.2.0.1
2af6c0f3f000-2af6c0f54000 r-xp 00000000 08:03 271558153 /usr/lib64/libz.so.1.2.7
2af6c0f54000-2af6c1153000 ---p 00015000 08:03 271558153 /usr/lib64/libz.so.1.2.7
2af6c1153000-2af6c1154000 r--p 00014000 08:03 271558153 /usr/lib64/libz.so.1.2.7
2af6c1154000-2af6c1155000 rw-p 00015000 08:03 271558153 /usr/lib64/libz.so.1.2.7
2af6c1155000-2af6c1157000 r-xp 00000000 08:03 268456705 /usr/lib64/libdl-2.17.so
2af6c1157000-2af6c1357000 ---p 00002000 08:03 268456705 /usr/lib64/libdl-2.17.so
2af6c1357000-2af6c1358000 r--p 00002000 08:03 268456705 /usr/lib64/libdl-2.17.so
2af6c1358000-2af6c1359000 rw-p 00003000 08:03 268456705 /usr/lib64/libdl-2.17.so
2af6c1359000-2af6c1360000 r-xp 00000000 08:03 270544427 /usr/lib64/librt-2.17.so
2af6c1360000-2af6c155f000 ---p 00007000 08:03 270544427 /usr/lib64/librt-2.17.so
2af6c155f000-2af6c1560000 r--p 00006000 08:03 270544427 /usr/lib64/librt-2.17.so
2af6c1560000-2af6c1561000 rw-p 00007000 08:03 270544427 /usr/lib64/librt-2.17.so
2af6c1561000-2af6c1753000 r-xp 00000000 08:11 54826594349 /home/yinbw-hgy/software/fftw3310_d/lib/libf ftw3.so.3.6.10
2af6c1753000-2af6c1952000 ---p 001f2000 08:11 54826594349 /home/yinbw-hgy/software/fftw3310_d/lib/libf ftw3.so.3.6.10
2af6c1952000-2af6c1963000 r--p 001f1000 08:11 54826594349 /home/yinbw-hgy/software/fftw3310_d/lib/libf ftw3.so.3.6.10
2af6c1963000-2af6c1964000 rw-p 00202000 08:11 54826594349 /home/yinbw-hgy/software/fftw3310_d/lib/libf ftw3.so.3.6.10
2af6c1964000-2af6c227c000 r-xp 00000000 08:03 539479607 /opt/intel2019/compilers_and_libraries_2019. 0.117/linux/mkl/lib/intel64_lin/libmkl_intel_lp64.so
2af6c227c000-2af6c247c000 ---p 00918000 08:03 539479607 /opt/intel2019/compilers_and_libraries_2019. 0.117/linux/mkl/lib/intel64_lin/libmkl_intel_lp64.so
2af6c247c000-2af6c247d000 r--p 00918000 08:03 539479607 /opt/intel2019/compilers_and_libraries_2019. 0.117/linux/mkl/lib/intel64_lin/libmkl_intel_lp64.so
2af6c247d000-2af6c2490000 rw-p 00919000 08:03 539479607 /opt/intel2019/compilers_and_libraries_2019. 0.117/linux/mkl/lib/intel64_lin/libmkl_intel_lp64.so
2af6c2490000-2af6c2495000 rw-p 00000000 00:00 0
2af6c2495000-2af6c44ff000 r-xp 00000000 08:03 539479608 /opt/intel2019/compilers_and_libraries_2019. 0.117/linux/mkl/lib/intel64_lin/libmkl_intel_thread.so
2af6c44ff000-2af6c46fe000 ---p 0206a000 08:03 539479608 /opt/intel2019/compilers_and_libraries_2019. 0.117/linux/mkl/lib/intel64_lin/libmkl_intel_thread.so
2af6c46fe000-2af6c4702000 r--p 02069000 08:03 539479608 /opt/intel2019/compilers_and_libraries_2019. 0.117/linux/mkl/lib/intel64_lin/libmkl_intel_thread.so
2af6c4702000-2af6c496c000 rw-p 0206d000 08:03 539479608 /opt/intel2019/compilers_and_libraries_2019. 0.117/linux/mkl/lib/intel64_lin/libmkl_intel_thread.so
2af6c496c000-2af6c4975000 rw-p 00000000 00:00 0
2af6c4975000-2af6c4b1d000 r-xp 00000000 08:03 1344986113 /opt/intel2019/compilers_and_libraries_2019. 0.117/linux/compiler/lib/intel64_lin/libiomp5.so
2af6c4b1d000-2af6c4d1c000 ---p 001a8000 08:03 1344986113 /opt/intel2019/compilers_and_libraries_2019. 0.117/linux/compiler/lib/intel64_lin/libiomp5.so
2af6c4d1c000-2af6c4d1f000 r--p 001a7000 08:03 1344986113 /opt/intel2019/compilers_and_libraries_2019. 0.117/linux/compiler/lib/intel64_lin/libiomp5.so
2af6c4d1f000-2af6c4d29000 rw-p 001aa000 08:03 1344986113 /opt/intel2019/compilers_and_libraries_2019. 0.117/linux/compiler/lib/intel64_lin/libiomp5.so
2af6c4d29000-2af6c4d58000 rw-p 00000000 00:00 0
2af6c4d58000-2af6c4e58000 r-xp 00000000 08:03 1208601194 /opt/intel2019/inspector_2019.0.0.569751/lib 64/libstdc++.so.6.0.20
2af6c4e58000-2af6c5057000 ---p 00100000 08:03 1208601194 /opt/intel2019/inspector_2019.0.0.569751/lib 64/libstdc++.so.6.0.20
2af6c5057000-2af6c5060000 r--p 000ff000 08:03 1208601194 /opt/intel2019/inspector_2019.0.0.569751/lib 64/libstdc++.so.6.0.20
2af6c5060000-2af6c5062000 rw-p 00108000 08:03 1208601194 /opt/intel2019/inspector_2019.0.0.569751/lib 64/libstdc++.so.6.0.20
2af6c5062000-2af6c5077000 rw-p 00000000 00:00 0
2af6c5077000-2af6c507e000 r-xp 00000000 08:03 272888373 /usr/lib64/libaec.so.0.0.10
2af6c507e000-2af6c527d000 ---p 00007000 08:03 272888373 /usr/lib64/libaec.so.0.0.10
2af6c527d000-2af6c527e000 r--p 00006000 08:03 272888373 /usr/lib64/libaec.so.0.0.10
2af6c527e000-2af6c527f000 rw-p 00007000 08:03 272888373 /usr/lib64/libaec.so.0.0.10
2af6c527f000-2af6c57c1000 rw-p 00000000 00:00 0
2af6c8000000-2af6c8021000 rw-p 00000000 00:00 0
2af6c8021000-2af6cc000000 ---p 00000000 00:00 0
7ffcd07b6000-7ffcd07d8000 rw-p 00000000 00:00 0 [stack]
7ffcd07d8000-7ffcd07da000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
[yinbw-hgy@master ~]$ pymolcas 834.input -oe 834.out -b 1
*** Error in `/home/yinbw-hgy/software/openmolcas2410_gmx/bin/gateway.exe': free(): invalid pointer: 0x000000000bb44310 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x81329)[0x2b07e3c17329]
/home/yinbw-hgy/software/gmx_qmmm/lib64/libgromacs_d.so.1(gmx_fio_close+0x11f)[0x2b07e1ef6a6f]
/home/yinbw-hgy/software/gmx_qmmm/lib64/libgromacs_d.so.1(read_tpx+0x6a)[0x2b07e1f2b9ba]
/home/yinbw-hgy/software/gmx_qmmm/lib64/libgromacs_d.so.1(_ZN3gmx7MMSlave7readTprEPKcP8_IO_FILE+0xda)[0x2b07e1ead25a]
/home/yinbw-hgy/software/gmx_qmmm/lib64/libgromacs_d.so.1(mmslave_read_tpr+0x15)[0x2b07e1ead3b5]
/home/yinbw-hgy/software/openmolcas2410_gmx/bin/gateway.exe[0x484fad]
/home/yinbw-hgy/software/openmolcas2410_gmx/bin/gateway.exe[0x41af09]
/home/yinbw-hgy/software/openmolcas2410_gmx/bin/gateway.exe[0x4053c5]
/home/yinbw-hgy/software/openmolcas2410_gmx/bin/gateway.exe[0x405165]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x2b07e3bb8555]
/home/yinbw-hgy/software/openmolcas2410_gmx/bin/gateway.exe[0x4051a1]
======= Memory map: ========
00400000-00569000 r-xp 00000000 08:11 35151177310 /home/yinbw-hgy/software/openmolcas2410_gmx/bin/gateway.exe
00768000-00769000 r--p 00168000 08:11 35151177310 /home/yinbw-hgy/software/openmolcas2410_gmx/bin/gateway.exe
00769000-0237c000 rw-p 00169000 08:11 35151177310 /home/yinbw-hgy/software/openmolcas2410_gmx/bin/gateway.exe
0237c000-0b08d000 rw-p 00000000 00:00 0
0bb41000-0bb8c000 rw-p 00000000 00:00 0 [heap]
2b07db167000-2b07db189000 r-xp 00000000 08:03 272045239 /usr/lib64/ld-2.17.so
2b07db189000-2b07db18b000 rw-p 00000000 00:00 0
2b07db1b8000-2b07db2fb000 rw-p 00000000 00:00 0
2b07db388000-2b07db389000 r--p 00021000 08:03 272045239 /usr/lib64/ld-2.17.so
2b07db389000-2b07db38a000 rw-p 00022000 08:03 272045239 /usr/lib64/ld-2.17.so
2b07db38a000-2b07db38b000 rw-p 00000000 00:00 0
2b07db38b000-2b07db625000 r-xp 00000000 08:03 272903697 /usr/lib64/libhdf5.so.8.0.1
2b07db625000-2b07db824000 ---p 0029a000 08:03 272903697 /usr/lib64/libhdf5.so.8.0.1
2b07db824000-2b07db829000 r--p 00299000 08:03 272903697 /usr/lib64/libhdf5.so.8.0.1
2b07db829000-2b07db830000 rw-p 0029e000 08:03 272903697 /usr/lib64/libhdf5.so.8.0.1
2b07db830000-2b07db831000 rw-p 00000000 00:00 0
2b07db831000-2b07dc075000 r-xp 00000000 08:03 539713629 /opt/intel2019/compilers_and_libraries_2019.0.117/linux/mkl/lib/intel64_lin/libmkl_gf_ilp64.so
2b07dc075000-2b07dc275000 ---p 00844000 08:03 539713629 /opt/intel2019/compilers_and_libraries_2019.0.117/linux/mkl/lib/intel64_lin/libmkl_gf_ilp64.so
2b07dc275000-2b07dc276000 r--p 00844000 08:03 539713629 /opt/intel2019/compilers_and_libraries_2019.0.117/linux/mkl/lib/intel64_lin/libmkl_gf_ilp64.so
2b07dc276000-2b07dc288000 rw-p 00845000 08:03 539713629 /opt/intel2019/compilers_and_libraries_2019.0.117/linux/mkl/lib/intel64_lin/libmkl_gf_ilp64.so
2b07dc288000-2b07dc28e000 rw-p 00000000 00:00 0
2b07dc28e000-2b07e0153000 r-xp 00000000 08:03 539479604 /opt/intel2019/compilers_and_libraries_2019.0.117/linux/mkl/lib/intel64_lin/libmkl_core.so
2b07e0153000-2b07e0353000 ---p 03ec5000 08:03 539479604 /opt/intel2019/compilers_and_libraries_2019.0.117/linux/mkl/lib/intel64_lin/libmkl_core.so
2b07e0353000-2b07e035a000 r--p 03ec5000 08:03 539479604 /opt/intel2019/compilers_and_libraries_2019.0.117/linux/mkl/lib/intel64_lin/libmkl_core.so
2b07e035a000-2b07e0388000 rw-p 03ecc000 08:03 539479604 /opt/intel2019/compilers_and_libraries_2019.0.117/linux/mkl/lib/intel64_lin/libmkl_core.so
2b07e0388000-2b07e03c7000 rw-p 00000000 00:00 0
2b07e03c7000-2b07e19e5000 r-xp 00000000 08:03 539713556 /opt/intel2019/compilers_and_libraries_2019.0.117/linux/mkl/lib/intel64_lin/libmkl_gnu_thread.so
2b07e19e5000-2b07e1be4000 ---p 0161e000 08:03 539713556 /opt/intel2019/compilers_and_libraries_2019.0.117/linux/mkl/lib/intel64_lin/libmkl_gnu_thread.so
2b07e1be4000-2b07e1be8000 r--p 0161d000 08:03 539713556 /opt/intel2019/compilers_and_libraries_2019.0.117/linux/mkl/lib/intel64_lin/libmkl_gnu_thread.so
2b07e1be8000-2b07e1c00000 rw-p 01621000 08:03 539713556 /opt/intel2019/compilers_and_libraries_2019.0.117/linux/mkl/lib/intel64_lin/libmkl_gnu_thread.so
2b07e1c00000-2b07e2a9f000 r-xp 00000000 08:11 54826571805 /home/yinbw-hgy/software/gmx_qmmm/lib64/libgromacs_d.so.1.0.0
2b07e2a9f000-2b07e2c9e000 ---p 00e9f000 08:11 54826571805 /home/yinbw-hgy/software/gmx_qmmm/lib64/libgromacs_d.so.1.0.0
2b07e2c9e000-2b07e2cad000 r--p 00e9e000 08:11 54826571805 /home/yinbw-hgy/software/gmx_qmmm/lib64/libgromacs_d.so.1.0.0
2b07e2cad000-2b07e2cd0000 rw-p 00ead000 08:11 54826571805 /home/yinbw-hgy/software/gmx_qmmm/lib64/libgromacs_d.so.1.0.0
2b07e2cd0000-2b07e2cdd000 rw-p 00000000 00:00 0
2b07e2cdd000-2b07e2dfc000 r-xp 00000000 08:03 268869255 /usr/lib64/libgfortran.so.3.0.0
2b07e2dfc000-2b07e2ffc000 ---p 0011f000 08:03 268869255 /usr/lib64/libgfortran.so.3.0.0
2b07e2ffc000-2b07e2ffd000 r--p 0011f000 08:03 268869255 /usr/lib64/libgfortran.so.3.0.0
2b07e2ffd000-2b07e2fff000 rw-p 00120000 08:03 268869255 /usr/lib64/libgfortran.so.3.0.0
2b07e2fff000-2b07e3100000 r-xp 00000000 08:03 268456707 /usr/lib64/libm-2.17.so
2b07e3100000-2b07e32ff000 ---p 00101000 08:03 268456707 /usr/lib64/libm-2.17.so
2b07e32ff000-2b07e3300000 r--p 00100000 08:03 268456707 /usr/lib64/libm-2.17.so
2b07e3300000-2b07e3301000 rw-p 00101000 08:03 268456707 /usr/lib64/libm-2.17.so
2b07e3301000-2b07e3326000 r-xp 00000000 08:03 268525118 /usr/lib64/libgomp.so.1.0.0
2b07e3326000-2b07e3525000 ---p 00025000 08:03 268525118 /usr/lib64/libgomp.so.1.0.0
2b07e3525000-2b07e3526000 r--p 00024000 08:03 268525118 /usr/lib64/libgomp.so.1.0.0
2b07e3526000-2b07e3527000 rw-p 00025000 08:03 268525118 /usr/lib64/libgomp.so.1.0.0
2b07e3527000-2b07e353d000 r-xp 00000000 08:03 1208601134 /opt/intel2019/inspector_2019.0.0.569751/lib64/libgcc_s.so.1
2b07e353d000-2b07e373d000 ---p 00016000 08:03 1208601134 /opt/intel2019/inspector_2019.0.0.569751/lib64/libgcc_s.so.1
2b07e373d000-2b07e373e000 rw-p 00016000 08:03 1208601134 /opt/intel2019/inspector_2019.0.0.569751/lib64/libgcc_s.so.1
2b07e373e000-2b07e3779000 r-xp 00000000 08:03 268600585 /usr/lib64/libquadmath.so.0.0.0
2b07e3779000-2b07e3978000 ---p 0003b000 08:03 268600585 /usr/lib64/libquadmath.so.0.0.0
2b07e3978000-2b07e3979000 r--p 0003a000 08:03 268600585 /usr/lib64/libquadmath.so.0.0.0
2b07e3979000-2b07e397a000 rw-p 0003b000 08:03 268600585 /usr/lib64/libquadmath.so.0.0.0
2b07e397a000-2b07e3991000 r-xp 00000000 08:03 270544421 /usr/lib64/libpthread-2.17.so
2b07e3991000-2b07e3b90000 ---p 00017000 08:03 270544421 /usr/lib64/libpthread-2.17.so
2b07e3b90000-2b07e3b91000 r--p 00016000 08:03 270544421 /usr/lib64/libpthread-2.17.so
2b07e3b91000-2b07e3b92000 rw-p 00017000 08:03 270544421 /usr/lib64/libpthread-2.17.so
2b07e3b92000-2b07e3b96000 rw-p 00000000 00:00 0
2b07e3b96000-2b07e3d5a000 r-xp 00000000 08:03 272045246 /usr/lib64/libc-2.17.so
2b07e3d5a000-2b07e3f59000 ---p 001c4000 08:03 272045246 /usr/lib64/libc-2.17.so
2b07e3f59000-2b07e3f5d000 r--p 001c3000 08:03 272045246 /usr/lib64/libc-2.17.so
2b07e3f5d000-2b07e3f5f000 rw-p 001c7000 08:03 272045246 /usr/lib64/libc-2.17.so
2b07e3f5f000-2b07e3f64000 rw-p 00000000 00:00 0
2b07e3f64000-2b07e3f66000 r-xp 00000000 08:03 272888375 /usr/lib64/libsz.so.2.0.1
2b07e3f66000-2b07e4165000 ---p 00002000 08:03 272888375 /usr/lib64/libsz.so.2.0.1
2b07e4165000-2b07e4166000 r--p 00001000 08:03 272888375 /usr/lib64/libsz.so.2.0.1
2b07e4166000-2b07e4167000 rw-p 00002000 08:03 272888375 /usr/lib64/libsz.so.2.0.1
2b07e4167000-2b07e417c000 r-xp 00000000 08:03 271558153 /usr/lib64/libz.so.1.2.7
2b07e417c000-2b07e437b000 ---p 00015000 08:03 271558153 /usr/lib64/libz.so.1.2.7
2b07e437b000-2b07e437c000 r--p 00014000 08:03 271558153 /usr/lib64/libz.so.1.2.7
2b07e437c000-2b07e437d000 rw-p 00015000 08:03 271558153 /usr/lib64/libz.so.1.2.7
2b07e437d000-2b07e437f000 r-xp 00000000 08:03 268456705 /usr/lib64/libdl-2.17.so
2b07e437f000-2b07e457f000 ---p 00002000 08:03 268456705 /usr/lib64/libdl-2.17.so
2b07e457f000-2b07e4580000 r--p 00002000 08:03 268456705 /usr/lib64/libdl-2.17.so
2b07e4580000-2b07e4581000 rw-p 00003000 08:03 268456705 /usr/lib64/libdl-2.17.so
2b07e4581000-2b07e4588000 r-xp 00000000 08:03 270544427 /usr/lib64/librt-2.17.so
2b07e4588000-2b07e4787000 ---p 00007000 08:03 270544427 /usr/lib64/librt-2.17.so
2b07e4787000-2b07e4788000 r--p 00006000 08:03 270544427 /usr/lib64/librt-2.17.so
2b07e4788000-2b07e4789000 rw-p 00007000 08:03 270544427 /usr/lib64/librt-2.17.so
2b07e4789000-2b07e497b000 r-xp 00000000 08:11 54826594349 /home/yinbw-hgy/software/fftw3310_d/lib/libfftw3.so.3.6.10
2b07e497b000-2b07e4b7a000 ---p 001f2000 08:11 54826594349 /home/yinbw-hgy/software/fftw3310_d/lib/libfftw3.so.3.6.10
2b07e4b7a000-2b07e4b8b000 r--p 001f1000 08:11 54826594349 /home/yinbw-hgy/software/fftw3310_d/lib/libfftw3.so.3.6.10
2b07e4b8b000-2b07e4b8c000 rw-p 00202000 08:11 54826594349 /home/yinbw-hgy/software/fftw3310_d/lib/libfftw3.so.3.6.10
2b07e4b8c000-2b07e54a4000 r-xp 00000000 08:03 539479607 /opt/intel2019/compilers_and_libraries_2019.0.117/linux/mkl/lib/intel64_lin/libmkl_intel_lp64.so
2b07e54a4000-2b07e56a4000 ---p 00918000 08:03 539479607 /opt/intel2019/compilers_and_libraries_2019.0.117/linux/mkl/lib/intel64_lin/libmkl_intel_lp64.so
2b07e56a4000-2b07e56a5000 r--p 00918000 08:03 539479607 /opt/intel2019/compilers_and_libraries_2019.0.117/linux/mkl/lib/intel64_lin/libmkl_intel_lp64.so
2b07e56a5000-2b07e56b8000 rw-p 00919000 08:03 539479607 /opt/intel2019/compilers_and_libraries_2019.0.117/linux/mkl/lib/intel64_lin/libmkl_intel_lp64.so
2b07e56b8000-2b07e56bd000 rw-p 00000000 00:00 0
2b07e56bd000-2b07e7727000 r-xp 00000000 08:03 539479608 /opt/intel2019/compilers_and_libraries_2019.0.117/linux/mkl/lib/intel64_lin/libmkl_intel_thread.so
2b07e7727000-2b07e7926000 ---p 0206a000 08:03 539479608 /opt/intel2019/compilers_and_libraries_2019.0.117/linux/mkl/lib/intel64_lin/libmkl_intel_thread.so
2b07e7926000-2b07e792a000 r--p 02069000 08:03 539479608 /opt/intel2019/compilers_and_libraries_2019.0.117/linux/mkl/lib/intel64_lin/libmkl_intel_thread.so
2b07e792a000-2b07e7b94000 rw-p 0206d000 08:03 539479608 /opt/intel2019/compilers_and_libraries_2019.0.117/linux/mkl/lib/intel64_lin/libmkl_intel_thread.so
2b07e7b94000-2b07e7b9d000 rw-p 00000000 00:00 0
2b07e7b9d000-2b07e7d45000 r-xp 00000000 08:03 1344986113 /opt/intel2019/compilers_and_libraries_2019.0.117/linux/compiler/lib/intel64_lin/libiomp5.so
2b07e7d45000-2b07e7f44000 ---p 001a8000 08:03 1344986113 /opt/intel2019/compilers_and_libraries_2019.0.117/linux/compiler/lib/intel64_lin/libiomp5.so
2b07e7f44000-2b07e7f47000 r--p 001a7000 08:03 1344986113 /opt/intel2019/compilers_and_libraries_2019.0.117/linux/compiler/lib/intel64_lin/libiomp5.so
2b07e7f47000-2b07e7f51000 rw-p 001aa000 08:03 1344986113 /opt/intel2019/compilers_and_libraries_2019.0.117/linux/compiler/lib/intel64_lin/libiomp5.so
2b07e7f51000-2b07e7f80000 rw-p 00000000 00:00 0
2b07e7f80000-2b07e8080000 r-xp 00000000 08:03 1208601194 /opt/intel2019/inspector_2019.0.0.569751/lib64/libstdc++.so.6.0.20
2b07e8080000-2b07e827f000 ---p 00100000 08:03 1208601194 /opt/intel2019/inspector_2019.0.0.569751/lib64/libstdc++.so.6.0.20
2b07e827f000-2b07e8288000 r--p 000ff000 08:03 1208601194 /opt/intel2019/inspector_2019.0.0.569751/lib64/libstdc++.so.6.0.20
2b07e8288000-2b07e828a000 rw-p 00108000 08:03 1208601194 /opt/intel2019/inspector_2019.0.0.569751/lib64/libstdc++.so.6.0.20
2b07e828a000-2b07e829f000 rw-p 00000000 00:00 0
2b07e829f000-2b07e82a6000 r-xp 00000000 08:03 272888373 /usr/lib64/libaec.so.0.0.10
2b07e82a6000-2b07e84a5000 ---p 00007000 08:03 272888373 /usr/lib64/libaec.so.0.0.10
2b07e84a5000-2b07e84a6000 r--p 00006000 08:03 272888373 /usr/lib64/libaec.so.0.0.10
2b07e84a6000-2b07e84a7000 rw-p 00007000 08:03 272888373 /usr/lib64/libaec.so.0.0.10
2b07e84a7000-2b07e89e9000 rw-p 00000000 00:00 0
2b07ec000000-2b07ec021000 rw-p 00000000 00:00 0
2b07ec021000-2b07f0000000 ---p 00000000 00:00 0
7ffe2ade7000-7ffe2ae09000 rw-p 00000000 00:00 0 [stack]
7ffe2aec9000-7ffe2aecb000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]Offline
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