abinit 6.10 +intel 12.1.0 + mkl  [SOLVED]

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roginovicci
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abinit 6.10 +intel 12.1.0 + mkl

Post by roginovicci » Fri Feb 10, 2012 3:18 pm

How should I compile abinit to force it use mkl library? I am using the following configure:

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./configure --prefix=/opt/abinit  --with-mpi-prefix=/opt/mpich  --enable-mpi --enable-mpi-io \                                 
--with-linalg-flavor=mkl \                                                                                                     
--with-linalg-libs="-L/opt/intel/mkl/lib/intel64 \                                                                             
-lmkl_intel_ilp64 -lmkl_intel_thread -lmkl_core -lmkl_cdft_core \                                                              
-lmkl_cdft_core  -lmkl_blacs_intelmpi_ilp64  -lmkl_lapack95_ilp64 \                                                            
-liomp5 -lpthread -lmkl_blas95_ilp641" \                                                                                       
--with-linalg-incs="-I/opt/intel/mkl/include" \                                                                                
--with-fft-flavor="fftw3-mkl" --with-fft-incs="-I/opt/intel/mkl/include/fftw" \                                                
 --with-fft-libs="-L/opt/intel/mkl/lib/intel64/fftw -lfftw3xf_intel" 


Compilation goes well but I get sigfault at runtime wile call from libmkl_intel_ilp64 library
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pouillon
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Re: abinit 6.10 +intel 12.1.0 + mkl

Post by pouillon » Fri Feb 10, 2012 5:02 pm

It might come from a bug in the compiler and/or MKL. You should recompile with lower optimization (e.g. --enable-optim=safe) and check whether the problem persists. If yes, you may even retry without optimization at all (--enable-optim=no). If your run still crashes, then I suggest you to send us your input file, so that we can determine whether your problem is reproducible and may come from Abinit.
Yann Pouillon
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Donostia-San Sebastián, Spain
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jbeuken
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Re: abinit 6.10 +intel 12.1.0 + mkl

Post by jbeuken » Fri Feb 10, 2012 8:40 pm

hello,

this .ac file is working with abinit 6.12.1 and with intel 11.1 under CentOS 5.7/xeon ( but it should be work with intel 12.1 )

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enable_gw_dpc = yes
enable_mpi = yes
enable_mpi_io = yes
with_mpi_prefix = /usr/local/openmpi_intel
with_dft_flavor = atompaw+bigdft+libxc+wannier90
with_fft_flavor = fftw3
with_fft_libs = -L/opt/intel/Compiler/11.1/current/mkl/lib/em64t -Wl,--start-group -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group -lpthread
with_linalg_flavor = mkl
with_linalg_libs = -L/opt/intel/Compiler/11.1/current/mkl/lib/em64t -Wl,--start-group -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group -lpthread


another config file with intel 12 but without MPI and with OpenMP


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FC = ifort
CC = icc
CXX = icpc
enable_gw_dpc = yes
enable_mpi = no
with_dft_flavor = atompaw+bigdft+libxc+wannier90
with_fft_flavor = fftw3
with_fft_libs = -L/opt/intel/composerxe/mkl/lib/intel64 -Wl,--start-group  -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -Wl,--end-group
with_linalg_flavor = mkl
with_linalg_libs = -L/opt/intel/composerxe/mkl/lib/intel64 -Wl,--start-group  -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -Wl,--end-group
FC_LDFLAGS_EXTRA = -openmp
FCFLAGS_EXTRA = -openmp
enable_smp = yes



regards

jmb
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Jean-Michel Beuken
Computer Scientist
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carsten.fortmann
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Re: abinit 6.10 +intel 12.1.0 + mkl

Post by carsten.fortmann » Thu Nov 22, 2012 9:28 am

I have similar issues with abinit 6.12.3 and mkl/intel v11.1/073:
here is my configure line (on linux 64bit environment) which is only slightly adjusted from the reply above (i.e. no mpi and no openmp)

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./configure \
--prefix=/usr/local \
--enable-64bit-flags \
--with-linalg-flavor=mkl \
--with-linalg-incs="-I/opt/intel/Compiler/11.1/073/mkl/include/" \
--with-linalg-libs="-L/opt/intel/Compiler/11.1/073/mkl/lib/em64t -Wl,--start-group -lmkl_intel_lp64 -lmkl_sequential -lmkl_lapack -lmkl_def -lmkl_core -Wl,--end-group -lpthread -lm" \
--with-fft-flavor="fftw3-mkl" \
--with-fft-incs="-I/opt/intel/Compiler/11.1/073/mkl/include/ -I/opt/intel/Compiler/11.1/073/mkl/include/fftw" \
--with-fft-libs="-L/opt/intel/Compiler/11.1/073/mkl/lib/em64t -Wl,--start-group -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group -lpthread -lfftw3xf_gnu" \
--enable-optim=safe
 \


./configure and make complete without issues, but

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~abinit/tests/> make tests


returns a segfault in the wannier90 test:

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echo "Running built-in test in_wannier90"
Running built-in test in_wannier90
timeout="0" perl ./Scripts/run-basic-tests.pl built-in in_wannier90 /home/cf/Downloads/abinit-6.12.3/tests
Segmentation fault (core dumped)

 Status file, with repetition rate  49, status number   295

  Level abinit         : call driver   
  Level driver         : call gstateimg
  Level gstateimg      : enter         
  Level gstate         : call scfcv    
  Level scfcv          : call outscfcv 
  istep      =    3


Adding

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--with-dft-flavor="libxc-fallback"
to the configure line helps.

Any clues? Any help is appreciated.
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Alain_Jacques
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Re: abinit 6.10 +intel 12.1.0 + mkl  [SOLVED]

Post by Alain_Jacques » Thu Nov 22, 2012 4:02 pm

To give you inspiration, please find below my config file to produce a reliable production abinit 6 with Intel 11.1 compiler. Mine with MPI - can be disabled easily -, without bigDFT - simply to spare some compilation time. To be used with --with-config-file= configure option.

Your fft-flavor and libs look suspicious; you have to use MKL fft, not MKL fftw3 calls.

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enable_64bit_flags="yes"
enable_mpi="yes"
enable_mpi_io="yes"
enable_debug="no"
enable_optim="aggressive"
enable_atmopaw="yes"
with_mpi_prefix=/opt/mpich2-1.3.2p1_ifc-11.1_m64
with_dft_flavor="atompaw+libxc+wannier90"
with_fft_flavor="fftw3"
with_fft_libs="-L/opt/intel/Compiler/11.1/073/mkl/lib/em64t -Wl,--start-group -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group -lpthread"
with_linalg_flavor="mkl"
with_linalg_libs="-L/opt/intel/Compiler/11.1/073/mkl/lib/em64t -Wl,--start-group -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group -lpthread"
enable_gw_dpc="yes"
AR=xiar
FC_LDFLAGS="-static"


Alain
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carsten.fortmann
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Re: abinit 6.10 +intel 12.1.0 + mkl

Post by carsten.fortmann » Mon Nov 26, 2012 12:34 pm

Code: Select all

with_fft_flavor="fftw3"


alain,

thanks for the hint, that did it.
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