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
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