Hello Sir,
It took some time but I could finally resolve the issue by enabling PLUMED to use it’s own ‘blas’ library.
But now I’m facing another error while using the ‘fix plumed’. It’s encountering a ‘segmentation fault’. I checked by switching off the ‘fix plumed’ line and it is running without any error.
For your kind information again, I’m using LAMMPS-7Aug19 with PLUMED2-2.4.7.
I did come across another thread where the same issue was asked and it was said that it has something to do with a bug in USER-PLUMED package. But, honestly, I couldn’t understand the solution.
Hello Sir,
It took some time but I could finally resolve the issue by enabling PLUMED to use it’s own ‘blas’ library.
But now I’m facing another error while using the ‘fix plumed’. It’s encountering a ‘segmentation fault’. I checked by switching off the ‘fix plumed’ line and it is running without any error.
For your kind information again, I’m using LAMMPS-7Aug19 with PLUMED2-2.4.7.
which are both outdated. if you are compiling from scratch, you should be using the latest versions.
I did come across another thread where the same issue was asked and it was said that it has something to do with a bug in USER-PLUMED package. But, honestly, I couldn’t understand the solution.
since you don’t point to the exact conversation, I cannot comment on it. however, there are no known bugs in fix plumed for the latest LAMMPS release (3 March 2020).
segmentation faults are very unspecific errors, often due to user input mistakes. so without tracking it down using a debugger, there is very little that can be said.
axel.
Sir,
I installed the latest version of lammps as you suggested. But error still persists. I tried to track the error through a debugger, and I’m getting the following:
Program received signal SIGSEGV, Segmentation fault.
0x0000000000000000 in ?? ()
Missing separate debuginfos, use: debuginfo-install glibc-2.12-1.149.el6.x86_64 numactl-devel-2.0.9-2.el6.x86_64 zlib-1.2.3-29.el6.x86_64
(gdb) where
#0 0x0000000000000000 in ?? ()
#1 0x0000000000df18a4 in PLMD::ActionWithValue::turnOnDerivatives() ()
#2 0x0000000000d23529 in PLMD::bias::Bias::Bias(PLMD::ActionOptions const&) ()
#3 0x0000000000d3ec02 in PLMD::bias::MetaD::MetaD(PLMD::ActionOptions const&) ()
#4 0x00000000010fc25f in PLMD::bias::MetaDRegisterMe439::create(PLMD::ActionOptions const&) ()
#5 0x0000000000de5d1b in PLMD::ActionRegister::create(PLMD::ActionOptions const&) ()
#6 0x0000000000e21fd8 in PLMD::PlumedMain::readInputWords(std::vector<std::__cxx11::basic_string<char, std::char_traits, std::allocator >, std::allocator<std::__cxx11::basic_string<char, std::char_traits, std::allocator > > > const&) ()
#7 0x0000000000e21a92 in PLMD::PlumedMain::readInputFile(std::__cxx11::basic_string<char, std::char_traits, std::allocator >) ()
#8 0x0000000000e24f86 in PLMD::PlumedMain::init() ()
#9 0x0000000000e1248c in PLMD::PlumedMain::cmd(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&, void*) ()
#10 0x0000000000e2547b in plumedmain_cmd ()
#11 0x0000000000824229 in LAMMPS_NS::FixPlumed::FixPlumed (this=0x2b926c0, lmp=0x7fffffff6850, narg=0, arg=0x2b92520) at …/fix_plumed.cpp:219
#12 0x000000000093b6cf in LAMMPS_NS::Modify::fix_creator (lmp=0x2b926c0, narg=-38832, arg=0x0) at …/modify.cpp:969
#13 0x0000000000932c1e in LAMMPS_NS::Modify::add_fix (this=0x2b926c0, narg=-38832, arg=0x0, trysuffix=45688096) at …/modify.cpp:903
#14 0x00000000008b6bfa in fix (this=0x2b926c0) at …/input.cpp:1587
#15 LAMMPS_NS::Input::execute_command (this=0x2b926c0) at …/input.cpp:817
#16 0x00000000008b8108 in LAMMPS_NS::Input::file (this=0x2b926c0) at …/input.cpp:229
#17 0x000000000090a64e in main (argc=3, argv=0x7fffffffcbc8) at …/main.cpp:65
This is very obviously from inside plumed and thus not a LAMMPS issue.