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psing51
Beginner
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NAMD MPIR_Thread: TLS definition in libmpi_mt.so section .tbss mismatches non-TLS definition in libmpi.so.12 section .bss

I am trying to compile namd(with smp) on centos 6.4 with intel 2015 for intel xeon phi , and i am getting following error:

MPIR_Thread: TLS definition in libmpi_mt.so section .tbss mismatches non-TLS definition in libmpi.so.12
section .bss could not read symbols: Bad value

attached :

  • namdmic.log : compilation error log
  • namd_build_smp.sh: namd compilation script

I tried this solution but then i got:

Adding file obj/psfplugin.o...
OpenMP support enabled
charmc> ----------- Module dependency search ------------
charmc> ----------- Module dependency search complete ------------
Adding registration for module NeighborLB
Adding registration for module HybridLB
Adding registration for module RefineLB
Adding registration for module GreedyLB
Adding registration for module CkMulticast
charmc: Executing mpicxx -m64 -fPIC -D_REENTRANT -D__CHARMC__=1 -DCMK_OPTIMIZE=1 -Iinc -Isrc -Ofast -fomit-frame-pointer -fp-model fast=2 -xHost -qopenmp -mt_mpi -offload-option,mic,compiler,-vec -offload-option,mic,compiler,-restrict -U_FORTIFY_SOURCE -fno-stack-protector -fopenmp -c moduleinit6026.C -o moduleinit6026.o
g++: fast=2: No such file or directory
g++: unrecognized option '-qopenmp'
g++: language Host not recognized
g++: language Host not recognized
Fatal Error by charmc in directory /home/puneet/NAMD_BUILD/NAMD_2.10_Source/Linux-x86_64-icc
   Command mpicxx -m64 -fPIC -D_REENTRANT -D__CHARMC__=1 -DCMK_OPTIMIZE=1 -Iinc -Isrc -Ofast -fomit-frame-pointer -fp-model fast=2 -xHost -qopenmp -mt_mpi -offload-option,mic,compiler,-vec -offload-option,mic,compiler,-restrict -U_FORTIFY_SOURCE -fno-stack-protector -fopenmp -c moduleinit6026.C -o moduleinit6026.o returned error code 1
charmc exiting...
rm -f moduleinit6026.C moduleinit6026.o
make: *** [namd2] Error 1

Eagerly awaiting your reply,

 

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1 Reply
TimP
Black Belt
182 Views

g++ doesn't support MPI on production Intel(r) Xeon Phi(tm).  Assuming you intended to use mpiicpc, you should check your initial build configuration. If you are using a non-Intel MPI which supports MIC via mpicxx, you should say so, but support channels for that MPI are more likely to be useful.

There is advice on this posted by Intel: https://software.intel.com/en-us/articles/namd-for-intel-xeon-phi-coprocessor

Questions about Intel MPI are more likely to find experts on the HPC and Cluster forum, or, since it is about MIC, that forum might be useful.

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