Hello,
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<patched namd directory>/Linux-x86_64-g++/namd2 +p1 +idlepoll ./namd.conf
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On 11 Jul 2017, at 12:26, Carlo Camilloni <carlo.c...@gmail.com> wrote:
Hi,Could you try to go back to the plumed version what was not working and apply this patch?
<namd_patch.patch>In the plumed2 folder you can typegit apply namd_patch.patch
And see if this solves your problem?Carlo
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<plumed_namd_test.tar.xz>
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<plumed_namd_test.tar.xz>
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<plumed_namd_test.tar.xz>
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Thread 1 "namd2" received signal SIGSEGV, Segmentation fault.
0x00007ffff77bf526 in PLMD::PlumedMain::update (this=0x16ce55c0) at PlumedMain.cpp:733
733 p->beforeUpdate();
728
729 stopwatch.start("6 Update");
730 // update step (for statistics, etc)
731 updateFlags.push(true);
732 for(const auto & p : actionSet) {
733 p->beforeUpdate();
734 if(p->isActive() && p->checkUpdate() && updateFlagsTop()) p->update();
735 }
736 while(!updateFlags.empty()) updateFlags.pop();
737 if(!updateFlags.empty()) plumed_merror("non matching changes in the update flags");
#0 0x00007ffff77bf526 in PLMD::PlumedMain::update (this=0x16ce55c0) at PlumedMain.cpp:733
#1 0x00007ffff77be63a in PLMD::PlumedMain::performCalc (this=0x16ce55c0) at PlumedMain.cpp:637
#2 0x00007ffff77b23e6 in PLMD::PlumedMain::cmd (this=0x16ce55c0, word="performCalc", val=0x0) at PlumedMain.cpp:207
#3 0x00007ffff77c5e79 in PLMD::WithCmd::cmd (this=0x16ce55c0, key="performCalc", val=0x0) at WithCmd.h:46
#4 0x00007ffff77c5b6b in plumedmain_cmd (plumed=0x16ce55c0, key=0x133b5ea "performCalc", val=0x0) at PlumedMainInitializer.cpp:52
#5 0x00007ffff79d8933 in plumed_cmd (p=..., key=0x133b5ea "performCalc", val=0x0) at Plumed.c:177
#6 0x00000000009c91b5 in PLMD::Plumed::cmd (this=0x16ce4f50, key=0x133b5ea "performCalc", val=0x0) at src/../Plumed.h:539
#7 0x00000000009b0a25 in GlobalMasterPlumed::easy_calc (this=0x16ce4e00) at src/ComputeMgr.C:242
#8 0x0000000000c867f6 in GlobalMasterEasy::calculate (this=0x16ce4e00) at src/GlobalMasterEasy.C:169
#9 0x0000000000c68405 in GlobalMaster::processData (this=0x16ce4e00, a_i=0x16e64380, a_e=0x16e64388, p_i=0x16e64240, g_i=0x0, g_e=0x0, gm_i=0x0, gm_e=0x0, gtf_i=0x0, gtf_e=0x0,
last_atoms_forced_i=0x0, last_atoms_forced_e=0x0, last_forces_i=0x0, forceid_i=0x0, forceid_e=0x0, totalforce_i=0x0) at src/GlobalMaster.C:47
#10 0x0000000000c6a17c in GlobalMasterServer::callClients (this=0x16ce4c10) at src/GlobalMasterServer.C:379
#11 0x0000000000c691ca in GlobalMasterServer::recvData (this=0x16ce4c10, msg=0x16e64270) at src/GlobalMasterServer.C:108
#12 0x00000000009b4704 in ComputeMgr::recvComputeGlobalData (this=0xc8769d0, msg=0x16e64270) at src/ComputeMgr.C:1454
#13 0x00000000009bcd35 in CkIndex_ComputeMgr::_call_recvComputeGlobalData_ComputeGlobalDataMsg (impl_msg=0x16e64270, impl_obj_void=0xc8769d0) at inc/ComputeMgr.def.h:2173
#14 0x0000000000ff8070 in CkDeliverMessageFree ()
#15 0x0000000000ffdb1c in _processHandler(void*, CkCoreState*) ()
#16 0x00000000010c7932 in CsdScheduleForever ()
#17 0x00000000010c7c9d in CsdScheduler ()
#18 0x00000000009097f4 in BackEnd::suspend () at src/BackEnd.C:292
#19 0x0000000000e9d1ad in ScriptTcl::suspend (this=0xc733c70) at src/ScriptTcl.C:72
#20 0x0000000000e9d386 in ScriptTcl::runController (this=0xc733c70, task=1) at src/ScriptTcl.C:110
#21 0x0000000000ea41a3 in ScriptTcl::run (this=0xc733c70) at src/ScriptTcl.C:2184
#22 0x00000000009047cc in after_backend_init (argc=2, argv=0x7fffffffd678) at src/mainfunc.C:178
#23 0x000000000090412f in main (argc=4, argv=0x7fffffffd678) at src/mainfunc.C:50
(gdb) print actionSet
$1 = (PLMD::ActionSet &) @0x16ce6990: {<std::vector<PLMD::Action*, std::allocator<PLMD::Action*> >> = std::vector of length 2, capacity 2 = {0xca08570, 0xca06bd0}, plumed = @0x16ce55c0}
(gdb) print (*actionSet)
Cannot resolve function operator* to any overloaded instance
(gdb) print actionSet[0]
$2 = (PLMD::Action *) 0xca08570
(gdb) print *actionSet[0]
$3 = {_vptr.Action = 0x0, name = "", label = "", line = std::vector of length 0, capacity 0, update_from = 1.7976931348623157e+308, update_until = 1.7976931348623157e+308,
after = std::vector of length 0, capacity 0, active = true, options = std::set with 0 elements, restart = false, doCheckPoint = false, plumed = @0x0, log = @0x0,
files = std::set with 0 elements, replica_index = 0, comm = @0x0, multi_sim_comm = @0x0, keywords = @0x0}
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