Re: [AMBER] compiling pmemd in amber9

From: Vijay Manickam Achari <vjrajamany.yahoo.com>
Date: Tue, 6 Dec 2011 10:50:37 +0000 (GMT)

Dear Sir Sorry for late reply because I was away from office. Well I have tried to re compile the PMEMD using the configure option as bellow for serial compilation: ./configure linux_em64t ifort nopar this also fails to compile as below:: ..... ..... ..... /mnt/data/cluster/intel/mkl/10.0.010/lib/em64t/libmkl_intel_thread.a(vml_threading_templates.o): In function `mkl_vml_service_openmp_get_num_procs': _tmp/treading_linux32e_intel_thread/vml_threading_templates.c:(.text+0x5022): undefined reference to `omp_get_num_procs' /mnt/data/cluster/intel/mkl/10.0.010/lib/em64t/libmkl_intel_thread.a(mkl_threading.o): In function `MKL_Get_Max_Threads': __tmp_mkl_threading.c:(.text+0x55): undefined reference to `omp_in_parallel' __tmp_mkl_threading.c:(.text+0x77): undefined reference to `omp_get_max_threads' make[1]: *** [pmemd] Error 1 make[1]: Leaving directory `/usr/local/amber9/src/pmemd/src' make: *** [all] Error 2 ptmlxclus:/usr/local/amber9/src/pmemd #  I attached the config.h file for your view. ( I have changed gcc to icc )   I am quite surprise why this serial compilation also fail.  Could you give some guide to solve this? Thanks in advance. Regards Vijay Manickam Achari (Phd Student) Chemistry Department, University of Malaya, 50603 Kuala Lumpur   vjramana.gmail.com ________________________________ From: David A. Case <case@biomaps.rutgers.edu> To: Vijay Manickam Achari <vjrajamany@yahoo.com>; AMBER Mailing List <amber@ambermd.org> Sent: Friday, 18 November 2011, 11:31 Subject: Re: [AMBER] compiling pmemd in amber9 On Fri, Nov 18, 2011, Vijay Manickam Achari wrote: > > > The machine that I am using is SGI_ALTIX XE1300... > > ptmlxclus:/mnt/data1/application/amber9/src/pmemd # cat /proc/cpuinfo  > processor: 0 > vendor_id: GenuineIntel > cpu family: 6 > model: 23 > model name: Intel(R) Xeon(R) CPU           X5272  @ 3.40GHz > > > Lastly I wanted to compile PMEMD and tried to do as ./configure > sgi_altix ifort mpi pubfft. I don't think you want sgi_altix here, as that probably refers to that ia64 altix machines, not the x86_64 configuration you have.  Leave out reference to MKL and try a more ordinary configuration option. ...hope this helps....dac _______________________________________________ AMBER mailing list AMBER@ambermd.org http://lists.ambermd.org/mailman/listinfo/amber

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Received on Tue Dec 06 2011 - 03:00:03 PST
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