I have installed charmm and have been trying to set up GSBP. As a start, I have taken the test files gsbptest1.inp from clongtest folder and the sccgsbp1_2cba.inp from the c32test folders (files attached). I am using the latest charmm version downloaded from the website.
In both the runs, the simulations crashed with a segmentation fault error. Following instructions in previous posts, I have compiled a debug version of charmm and for the corresponding output. The error is as follows:
" Backtrace for this error: #0 0x7fee320e42da in ??? #1 0x7fee320e3503 in ??? #2 0x7fee31760f1f in ??? #3 0x55a7716449e6 in sphe_stpol at /home/sridhar/charmm_debug/charmm/source/misc/pbeq.F90:16141 #4 0x55a7716afb93 in __pbeq_MOD_gsbp0 at /home/sridhar/charmm_debug/charmm/source/misc/pbeq.F90:954 #5 0x55a7716b8202 in __pbeq_MOD_pbeq0 at /home/sridhar/charmm_debug/charmm/source/misc/pbeq.F90:469 #6 0x55a770d58ced in maincomx_ at /home/sridhar/charmm_debug/charmm/source/charmm/charmm_main.F90:1151 #7 0x55a770d5b5eb in charmm at /home/sridhar/charmm_debug/charmm/source/charmm/charmm_main.F90:396 #8 0x55a770d5b62c in main at /home/sridhar/charmm_debug/charmm/source/charmm/charmm_main.F90:2 Segmentation fault (core dumped)
In both cases, the program is failing at the same lines in the code. I am wondering if it is the version of charmm or it has something to do with the input file.
Kindly suggest any changes in version/input script.
A seg fault is usually a coding error of some kind, either an outright error, or perhaps insufficient checks for bad data values, etc. The "invalid memory reference" message suggests it may be a legitimate bug.
It could also be an issue with how the program was built, i.e. compiler suite and version, parallel (mpi) library and version, and command line options used with either install.com or configure. It would be helpful to provide these names and versions. (Note that the GCC suite that comes with a Linux distribution may not be the best choice.)
Since these are test cases in principle they should work, but the ones in clongtest may not have been evaluated by the developers in quite a while, and the other one depends on SCCDFTB, which most developers are probably not using for routine testing. You should probably run the full test suite, as that may help pin down what the cause might be.
I have installed charmm versions using the command "./install.com gnu T" and "./install.com gnu T +DFTBMKL debug". with the default GCC (gcc (Ubuntu 7.4.0-1ubuntu1~18.04.1) 7.4.)
Both these versions did run for other calculations, including running dynamics with GSBP, where I was able to provide the input .mij and .pjix commands. Also, the SCCDFTB calculations were also running without any issues (in a case where set up of GSBP was not involved).