Hi,
Recently, I would like to try out the function of Reaxff in Amber. I built
the openMPI version of MPI with the modification of these cmake parameters
in run_cmake. (I added the following things: -DBUILD_REAXFF_PUREMD=TRUE
-DBUILD_QUICK=TRUE
-DCUDA=TRUE
-DBUILD_GUI=TRUE
-DOPENMP=TRUE)
When I ran make install, I got the error message...
CMake Error at
/home/ikki/Documents/amber20_src/cmake/FixCondaShebang/FixCondaShebang.cmake:26
(file): file failed to open for reading (No such file or directory):
/home/ikki/Documents/amber20//bin/amber.pip
I searched some articles from the mail list. Someone stated that it can be
ignored.
So, I tried to run the make test.parallel with export DO_PARALLEL="mpirun
-np 8".
However, I got lots of errors: failed to start the process. All the tests
failed... Because I installed the openMP version, will this be the issue?
I tried to run make test.serial instead. Everything seems to be fine, but
with 3 errors.
The last part of test is:
Summary of AmberTools serial tests:
2733 file comparisons passed
3 file comparisons failed (2 of which can be ignored)
1 tests experienced errors
Test log file saved as
/home/ikki/Documents/amber20///logs/test_at_serial/2021-12-10_15-04-04.log
Test diffs file saved as
/home/ikki/Documents/amber20///logs/test_at_serial/2021-12-10_15-04-04.diff
Therefore, I tried to find the problems.
The most important error is the failure on Reaxff...
It gave me the following error:
cd qmmm_EXTERN/pure_QM_MD_MRCC && ./Run.h2o.blyp_6-31g_md
MRCC not installed - Skipping Test...
Program received signal SIGSEGV: Segmentation fault - invalid memory
reference.
Backtrace for this error:
#0 0x7fc7f8994d5a
#1 0x7fc7f8993ef5
#2 0x7fc7f87ad20f
#3 0x7fc7f87e0a26
#4 0x7fc7f88981b2
#5 0x7fc7fb4401f3
#6 0x7fc7fb46474d
#7 0x55a67f5a1c80
#8 0x55a67f560608
#9 0x55a67f5515aa
#10 0x55a67f3eebfe
#11 0x55a67f481f7f
#12 0x55a67f436444
#13 0x55a67f42f68c
#14 0x55a67f42f6e8
#15 0x7fc7f878e0b2
#16 0x55a67f27ddcd
#17 0xffffffffffffffff
Segmentation fault (core dumped)
./Run.benz_water_md.reaxff: Program error
make[2]: *** [Makefile:795: test.sander.EXTERN] Error 1
diffing h2o.blyp_6-31g.out.save with h2o.blyp_6-31g.out
PASSED
==============================================================
The other errors are:
cd sanderapi && make test
make[3]: Entering directory '/home/ikki/Documents/amber20/test/sanderapi'
(if [ -f "/home/ikki/Documents/amber20///lib/libsander.so" ]; then \
make test_all; \
else \
make test_none; \
fi;)
make[4]: Entering directory '/home/ikki/Documents/amber20/test/sanderapi'
Creating the bad prmtop test.parm7
Testing the Fortran API
/bin/gfortran -Wall -Wno-tabs -Wno-unused-function -ffree-line-length-none
-Wno-unused-dummy-argument -Wno-unused-variable
-I/home/ikki/Documents/amber20///include -L/home/ikki/Documents/am>
Running testf
Testing proper treatment of a bad prmtop; an error message is expected:
ERROR: Flag "ATOM_NAME" not found in PARM file
PASSED
==============================================
And...
Testing the C API
/bin/gcc -Wall -Wno-unused-function -Wno-unknown-pragmas
-Wno-unused-variable -Wno-unused-but-set-variable
-I/home/ikki/Documents/amber20///include
-L/home/ikki/Documents/amber20///lib tes>
test.c: In function ‘main’:
test.c:163:5: warning: ‘strncpy’ output truncated before terminating nul
copying 3 bytes from a string of the same length [-Wstringop-truncation]
163 | strncpy(qmmm_options.qm_theory, "PM3", 3);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
test.c:207:5: warning: ‘strncpy’ output truncated before terminating nul
copying 4 bytes from a string of the same length [-Wstringop-truncation]
207 | strncpy(qmmm_options.qmmask, ":1-2", 4);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
test.c:208:5: warning: ‘strncpy’ output truncated before terminating nul
copying 8 bytes from a string of the same length [-Wstringop-truncation]
208 | strncpy(qmmm_options.qm_theory, "PDDG-PM3", 8);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
test.c:248:9: warning: ‘strncpy’ output truncated before terminating nul
copying 4 bytes from a string of the same length [-Wstringop-truncation]
248 | strncpy(qmmm_options.qmmask, ":1-2", 4);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
test.c:249:9: warning: ‘strncpy’ output truncated before terminating nul
copying 4 bytes from a string of the same length [-Wstringop-truncation]
249 | strncpy(qmmm_options.qm_theory, "DFTB", 4);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Running testc
Testing proper treatment of a bad prmtop; an error message is expected:
ERROR: Flag "ATOM_NAME" not found in PARM file
PASSED
==================================================
make[2]: Target 'test.serial' not remade because of errors.
make[2]: Leaving directory '/home/ikki/Documents/amber20/test'
make[2]: Entering directory '/home/ikki/Documents/amber20/test'
cd 2048_wat_gem && ./Run.2048_wat_nvt_gem.pmemd.gem
diffing mdout.2048_wat_nvt_gem.pmemd.gem.save with
mdout.2048_wat_nvt_gem.pmemd.gem
PASSED
==============================================================
Can these errors be ignored? I really want to use Reaxff to simulate the
bond forming and breaking between two small molecules. Additionally, can
you give me some advice on how to analyze and visualize the results of
Reaxff MD?
Can QM/MM produce the trajectory file showing the bond forming and breaking
in the trajectory file?
Thank you very much!
--
Best regards,
Shang-Wei Li
Graduate Institute of Cancer Biology and Drug Discovery, Taipei Medical
University
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Received on Tue Dec 28 2021 - 18:00:02 PST
