02 February 2016 2 5K Report

Hi,

I patched gromacs 5.0.2 with plumed 2.2.1 (version meant for gromacs 5.0.4) and I am trying to run the belfast tutorial. While starting the simulation and running the mdrun -plumed, I get this error (without any output):

[node185:18617] mca: base: component_find: unable to open /cm/shared/apps/openmpi/gcc/64/1.4.4/lib64/openmpi/mca_plm_tm: perhaps a missing symbol, or compiled for a different version of Open MPI? (ignored)

[node185:18617] mca: base: component_find: unable to open /cm/shared/apps/openmpi/gcc/64/1.4.4/lib64/openmpi/mca_ras_tm: perhaps a missing symbol, or compiled for a different version of Open MPI? (ignored)

********** STACK DUMP **********

********** STACK DUMP **********

********** STACK DUMP **********

********** STACK DUMP **********

mdrun(_ZN4PLMD9Exception28abortIfExceptionsAreDisabledEv+0x41) [0x6d7421]

mdrun(_ZN4PLMD9ExceptionC2ERKSsS2_jS2_+0x38) [0x6d7908]

mdrun(_ZN4PLMD10vesselbase14VesselRegister3addESsPFPNS0_6VesselERKNS0_13VesselOptionsEEPFvRNS_8KeywordsEESC_+0x248) [0x750bd8]

mdrun() [0x74d329]

mdrun() [0x7df706]

******** END STACK DUMP ********

mdrun(_ZN4PLMD9Exception28abortIfExceptionsAreDisabledEv+0x41) [0x6d7421]

mdrun(_ZN4PLMD9ExceptionC2ERKSsS2_jS2_+0x38) [0x6d7908]

mdrun(_ZN4PLMD10vesselbase14VesselRegister3addESsPFPNS0_6VesselERKNS0_13VesselOptionsEEPFvRNS_8KeywordsEESC_+0x248) [0x750bd8]

mdrun() [0x74d329]

mdrun() [0x7df706]

******** END STACK DUMP ********

mdrun(_ZN4PLMD9Exception28abortIfExceptionsAreDisabledEv+0x41) [0x6d7421]

mdrun(_ZN4PLMD9ExceptionC2ERKSsS2_jS2_+0x38) [0x6d7908]

mdrun(_ZN4PLMD10vesselbase14VesselRegister3addESsPFPNS0_6VesselERKNS0_13VesselOptionsEEPFvRNS_8KeywordsEESC_+0x248) [0x750bd8]

mdrun() [0x74d329]

mdrun() [0x7df706]

******** END STACK DUMP ********

+++ Internal PLUMED error

+++ file VesselRegister.cpp, line 51

+++ message: assertion failed m.count(keyword)==0, keyword has already been registered

+++ Internal PLUMED error

+++ file VesselRegister.cpp, line 51

+++ message: assertion failed m.count(keyword)==0, keyword has already been registered

+++ Internal PLUMED error

+++ file VesselRegister.cpp, line 51

+++ message: assertion failed m.count(keyword)==0, keyword has already been registered

mdrun(_ZN4PLMD9Exception28abortIfExceptionsAreDisabledEv+0x41) [0x6d7421]

mdrun(_ZN4PLMD9ExceptionC2ERKSsS2_jS2_+0x38) [0x6d7908]

mdrun(_ZN4PLMD10vesselbase14VesselRegister3addESsPFPNS0_6VesselERKNS0_13VesselOptionsEEPFvRNS_8KeywordsEESC_+0x248) [0x750bd8]

mdrun() [0x74d329]

mdrun() [0x7df706]

******** END STACK DUMP ********

+++ Internal PLUMED error

+++ file VesselRegister.cpp, line 51

+++ message: assertion failed m.count(keyword)==0, keyword has already been registered

--------------------------------------------------------------------------

mpirun noticed that process rank 0 with PID 18618 on node node185 exited on signal 6 (Aborted).

--------------------------------------------------------------------------

Can someone please help me out here resolving this issue?

Kindly,

Swapnil

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