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Tempeh_R_
Beginner
128 Views

Problem using mpirun

Hello, It's my first time posting in these forums and I hope that you can help me. I'm trying to run VASP (which uses FORTRAN 90) using Fedora 14 (Laughlin) on an Intel Xeon E5430 Processor and I run into the error message below: [hamad@local 1_1_O_atom]$ mpirun /home2/hamad/VASPfiles/Vasp/vasp.5.3/vasp& [1] 19852 [hamad@local 1_1_O_atom]$ vasp.5.3.3 18Dez12 (build Sep 24 2015 19:33:17) complex POSCAR found : 1 types and 1 ions /home2/hamad/VASPfiles/Vasp/vasp.5.3/vasp: symbol lookup error: /home2/hamad/VASPfiles/Vasp/vasp.5.3/vasp: undefined symbol: mkl_serv_set_progress_interface -------------------------------------------------------------------------- mpirun noticed that the job aborted, but has no info as to the process that caused that situation. -------------------------------------------------------------------------- Using mpirun also yields the same error message as above. If it helps this is the Processor information I get from the command line: [hamad@local ~]$ cat /proc/cpuinfo | grep vendor | uniq vendor_id : GenuineIntel [hamad@local ~]$ cat /proc/'model name' | uniq cat: /proc/model name: No such file or directory [hamad@local ~]$ cat /proc/cpuinfo | grep 'model name' | uniq model name : Intel(R) Xeon(R) CPU E5430 @ 2.66GHz [hamad@local ~]$ lscpu Architecture: x86_64 CPU op-mode(s): 32-bit, 64-bit CPU(s): 8 Thread(s) per core: 1 Core(s) per socket: 4 CPU socket(s): 2 NUMA node(s): 1 Vendor ID: GenuineIntel CPU family: 6 Model: 23 Stepping: 6 CPU MHz: 2659.612 Virtualization: VT-x L1d cache: 32K L1i cache: 32K L2 cache: 6144K NUMA node0 CPU(s): 0-7 Any help towards understanding the meaning of the error message and how to fix it will be greatly appreciated. Thank you in advance for all your help.
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8 Replies
Evarist_F_Intel
Employee
128 Views

Hello Tempeh,

Could you please share the link line you used for building VASP? And could please also show the ldd output for VASP binary:

$ ldd /home2/hamad/VASPfiles/Vasp/vasp.5.3/vasp

 

Tempeh_R_
Beginner
128 Views

Hello Evarist, I'm not the person that built VASP, so I don't know what link line they used (and I think that the person isn't working at the lab anymore). Is there anything I can do to find out? EDIT: I checked the command history on the terminal and I see the following commands (from oldest to newest): cd /opt/intel/Compiler/11.1/0.73/mkl/interfaces/fftw3xf su cd /home2/hamad/VASPfiles/Vasp cd vasp.5.3.mpi cp /media/KINGSTON/Makefile-vasp-intel-11-RH ./Makefile vi Makefile make clean cp Makefile makefile make vasp which mpif90 make clean vi Makefile cp Makefile makefile make vasp ls -l vasp cp makefile /media/KINGSTON/makefile-vasp-11.1-073 I did run the command, and the ldd output is the following: [hamad@local ~]$ ldd /home2/hamad/VASPfiles/Vasp/vasp.5.3/vasp linux-vdso.so.1 => (0x00007ffff03ff000) libguide.so => /opt/intel/Compiler/11.1/073/lib/intel64/libguide.so (0x00002b43139ed000) libmkl_intel_lp64.so => /opt/intel/Compiler/11.1/073/mkl/lib/em64t/libmkl_intel_lp64.so (0x00002b4313bbf000) libmkl_intel_thread.so => /opt/intel/Compiler/11.1/073/mkl/lib/em64t/libmkl_intel_thread.so (0x00002b43140bb000) libmkl_core.so => /opt/intel/Compiler/11.1/073/mkl/lib/em64t/libmkl_core.so (0x00002b43154f7000) libiomp5.so => /opt/intel/Compiler/11.1/073/lib/intel64/libiomp5.so (0x00002b43159af000) libm.so.6 => /lib64/libm.so.6 (0x000000390f200000) libpthread.so.0 => /lib64/libpthread.so.0 (0x000000390f600000) libc.so.6 => /lib64/libc.so.6 (0x000000390ee00000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x0000003910600000) libdl.so.2 => /lib64/libdl.so.2 (0x000000390fa00000) /lib64/ld-linux-x86-64.so.2 (0x000000390ea00000) Thanks again!
Ying_H_Intel
Employee
128 Views

Hi Tempeh R. Could you please check if the mkl_serv_set_progress_interface are from mkl library for example, >cd /opt/intel/Compiler/11.1/073/mkl/lib/em64t >nm libmkl_intel_thread.so|grep mkl_serv_set_progress_interface I recalled one post in the forum, may be help. https://software.intel.com/en-us/forums/intel-math-kernel-library/topic/351714 If the symboy are coming from MKL, then either rebuild the vasp with --no-as-needed option (you mentioned, the build is other person) or use LD_PRELOAD=opt/intel/mkl/lib/intel64/libmkl_intel_thread.so:opt/intel/mkl/lib/intel64/libmkl_core.so: /opt/intel/Compiler/11.1/073/lib/intel64/libiomp5.so , then run the mpirun. Best Regards, Ying
Tempeh_R_
Beginner
128 Views

I ran cd /opt/intel/Compiler/11.1/073/mkl/lib/em64t nm libmkl_intel_thread.so|grep mkl_serv_set_progress_interface and I get no message output, so I assume it's no errors. After running the those two commands I ran: LD_PRELOAD=opt/intel/mkl/lib/intel64/libmkl_intel_thread.so:opt/intel/mkl/lib/intel64/libmkl_core.so: /opt/intel/Compiler/11.1/073/lib/intel64/libiomp5.so and I get the following message: Segmentation fault (core dumped) What does this message mean and what should I do in this case? If I should try to rebuild VASP, where would I use the --no-as-needed option? (I will post in the VASP forums also asking how to build it, since I think that might be beyond the scope of this forum). Thank you again for all your help and I apologize for my inexperience.
Ying_H_Intel
Employee
128 Views

Hello  Tempeh,

cd /opt/intel/Compiler/11.1/073/mkl/lib/em64t
nm libmkl_intel_thread.so|grep mkl_serv_set_progress  and I get no message output,

This means the symbol mkl_serv_set_progress_interface  is not in the libmkl_intel_thread.so. Could you please check other mkl library and see which library include the symbols? 

we haven't 073 installed, so can't check. ( I had other 11.1 version, but haven't found the symbol either).

As we haven't found the symbol in some library so far,  so you may try any one or any combination : LD_PRELOAD=opt/intel/mkl/lib/intel64/libmkl_intel_thread.so:opt/intel/mkl/lib/intel64/libmkl_core.so and see if any changes.

Best Regards
Ying

 

 

 

Tempeh_R_
Beginner
128 Views

How can I check other mkl libraries?
Evarist_F_Intel
Employee
128 Views

Tempeh,

It looks like you use quite old version of MKL... Could you please check the exact version of MKL by looking at the file /opt/intel/Compiler/11.1/073/mkl/include/mkl.h and post it here (see __INTEL_MKL__, __INTEL_MKL_MINOR__, __INTEL_MKL_UPDATE__ defines)?

Could you please also grep the VASP source files and check whether them call mkl_serv_set_progress_interface?

$ grep -i set_progress_interface $VASP_SOURCE_DIR

 

Ying_H_Intel
Employee
128 Views

Hi Tempeh,

you can check other mkl libraries like below: 

[yhu5@snb01 em64t]$ cd /opt/intel/Compiler/11.1/075/mkl/lib/em64t

[yhu5@snb01 em64t]$nm -gA *.so | grep mkl_serv_set_progress

libmkl_gf_ilp64.so:                 U mkl_serv_set_progress
libmkl_gf_lp64.so:                 U mkl_serv_set_progress
libmkl_gnu_thread.so:00000000001c7190 T mkl_serv_set_progress
libmkl_intel_ilp64.so:                 U mkl_serv_set_progress
libmkl_intel_lp64.so:                 U mkl_serv_set_progress
libmkl_intel_sp2dp.so:                 U mkl_serv_set_progress
libmkl_intel_thread.so:00000000002245e0 T mkl_serv_set_progress
libmkl_pgi_thread.so:00000000001c9c20 T mkl_serv_set_progress
libmkl_sequential.so:00000000001b8df0 T mkl_serv_set_progress
i'm using 11.1.075. There is no symbol. 

Let's see the result of the symbols as Evarist suggested. 

Regards,

Ying 

 

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