Abinit-7.2.1 compilation error with fftw3-mkl  [SOLVED]

option, parallelism,...

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Abinit-7.2.1 compilation error with fftw3-mkl

Post by letuan » Fri Apr 05, 2013 9:26 am

Hi everyone,
I browsed the topic but did not see the similar (by my very few experience) error so I would like to get a help. I use IBM x3550, 2xXeon 5230 QC, 8 GB RAM with Scientific Linux 6.4, Intel Parallel Studio XE 2013 Update 3, OpenMPI-1.6.4.
Recently I decided to reinstall Abinit with using FFT3 parallelism. The compilation with the following option returned value 0, though some messages still in config.log attached hereby:

Code: Select all

./configure FC=/usr/local/bin/mpif90 CC=icc --with-trio-flavor="none" --with-dft-flavor="none" --with-linalg-flavor="mkl" --with-linalg-libs="-L/opt/intel/mkl/lib/intel64/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lmkl_blas95_lp64 -lmkl_lapack95_lp64" --with-linalg-incs="-I/opt/intel/mkl/lib/intel64/" --enable-mpi --with-fft-flavor="fftw3-mkl" --with-fft-incs="-I/opt/intel/mkl/include/fftw" --with-fft-libs="-L/opt/intel/mkl/interfaces/fftw3xf -lfftw3xf_intel"

Before the compiling, I have to build the library for fftw3 wrappers in Intel package by entering into /opt/intel/mkl/interfaces/fftw3xf and issuing command

Code: Select all

make libintel64 compiler=intel
. But I ran into this error for many times:

Code: Select all

/usr/local/bin/mpif90 -DHAVE_CONFIG_H -I. -I../.. -I../../src/incs -I../../src/incs -I/home/letuan/Programs/abinit-7.2.1/fallbacks/exports/include   -free -module /home/letuan/Programs/abinit-7.2.1/src/mods  -O2 -xHost -g -extend-source -vec-report0 -noaltparam -nofpscomp   -c -o prep_nonlop.o prep_nonlop.F90
0_10711

: catastrophic error: **Internal compiler error: internal abort** Please report this error along with the circumstances in which it occurred in a Software Problem Report.  Note: File and line given may not be explicit cause of this error.
compilation aborted for prep_fourwf.F90 (code 1)
make[4]: *** [prep_fourwf.o] Error 1
make[4]: *** Waiting for unfinished jobs....
make[4]: Leaving directory `/home/letuan/Programs/abinit-7.2.1/src/66_wfs'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory `/home/letuan/Programs/abinit-7.2.1/src'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/letuan/Programs/abinit-7.2.1'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/letuan/Programs/abinit-7.2.1'
make: *** [multi] Error 2

Please, help me to overcome this difficulty.
Thanks a lot
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Re: Abinit-7.2.1 compilation error with fftw3-mkl

Post by jbeuken » Fri Apr 05, 2013 6:12 pm

Hi

this is my recipe ( build.ac file ) to use fftw3 from mkl.11 with intel 12.1.4
( config use nightly with our abinit test farm : http://www.abinit.org/developers/dev-environment/buildbot/buildbot-builder-matrix)

Code: Select all

enable_gw_dpc = yes
enable_mpi = yes
enable_mpi_io = yes
with_mpi_prefix = /usr/local/openmpi_intel12
with_dft_flavor = atompaw+bigdft+libxc+wannier90
with_trio_flavor = netcdf+etsf_io+fox
with_fft_flavor = fftw3
with_fft_libs = -L/opt/intel/composerxe/mkl/lib/intel64 -Wl,--start-group  -lmkl_intel_lp64 -lmkl_sequential -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_sequential -lmkl_core -Wl,--end-group


run :

Code: Select all

./configure --with-config-file=./build.ac



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Re: Abinit-7.2.1 compilation error with fftw3-mkl

Post by jbeuken » Fri Apr 05, 2013 10:42 pm

Hi,

I try also with intel 13.1.1 and openmpi 1.6.4
and I have the same problem ( "catastrophic error: **Internal compiler error: internal abort**" ) !

it seems that the compiler has problem to compile "src/66_wfs/prep_fourwf.F90" with -O3 optimization
with -O1 , it works !

this is my new build.ac with the "fcflags_opt_66_wfs" to prevent compilation with -O3 under this folder :

Code: Select all

enable_gw_dpc = yes
enable_mpi = yes
enable_mpi_io = yes
with_mpi_prefix = /usr/local/openmpi_intel13
with_dft_flavor = atompaw+bigdft+libxc+wannier90
with_trio_flavor = netcdf+etsf_io+fox
fcflags_opt_66_wfs = -O1 -xHost -g -extend-source -vec-report0 -noaltparam -nofpscomp
with_fft_flavor = fftw3
with_fft_libs = -L/opt/intel/composer_xe_2013.3.163/mkl/lib/intel64 -Wl,--start-group  -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group
with_linalg_flavor = mkl
with_linalg_libs = -L/opt/intel/composer_xe_2013.3.163/mkl/lib/intel64 -Wl,--start-group  -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group


all tests succeed 8-)

Code: Select all

=============================================================================================
Tests SEQ start at 21:51 and done after     1736s 
=============================================================================================
     Serie  #tests  #succes  #passed  #failed  #missing  | #timed   #CPU    #WALL  %WALL | T
=============================================================================================
   atompaw     2        1       1       0          0     |    2      7.5      7.5    0.1 | 4
    bigdft    22       19       3       0          0     |   22    254.4    254.8    4.8 | 3
   etsf_io     8        8       0       0          0     |    7     14.2     14.3    0.3 | 4
      fast    28       28       0       0          0     |   26     33.3     33.6    0.6 | 3
       fox     2        1       1       0          0     |    2     86.0     86.1    1.6 | 3
     libxc    21       14       7       0          0     |   20    200.7    201.5    3.8 | 2
 tutoplugs      4        0       4       0          0     |    4     14.8     14.8    0.3 | 4
tutorespfn    47       34      13       0          0     |   39    930.8    934.7   17.4 | 3
  tutorial    62       44      18       0          0     |   60    669.7    672.3   12.5 | 1
   unitary     4        4       0       0          0     |    0      0.0      0.0    0.0 | 0
        v1    97       96       1       0          0     |   97    180.2    181.7    3.4 | 1
        v2    95       83      12       0          0     |   75    232.5    233.3    4.4 | 2
        v3    92       80      12       0          0     |   87    365.7    367.4    6.9 | 3
        v4    94       73      21       0          0     |   73    391.3    393.1    7.3 | 4
        v5   100       71      29       0          0     |   91    794.8    799.3   14.9 | 4
   v67mbpt    30       25       5       0          0     |   17    222.1    223.2    4.2 | 1
        v6    81       66      15       0          0     |   70    598.5    602.6   11.2 | 2
        v7    22       15       7       0          0     |   18    294.2    295.5    5.5 | 2
     vdwxc     1        1       0       0          0     |    1     13.1     13.1    0.2 | 4
 wannier90      6        0       6       0          0     |    6     29.2     29.3    0.5 | 4
---------------------------------------------------------------------------------------------
     paral    70       53      17       0          0     |   70    741.3    744.7
     mpiio    12        9       3       0          0     |   12     86.5     92.8
=============================================================================================


jmb
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Re: Abinit-7.2.1 compilation error with fftw3-mkl

Post by letuan » Sat Apr 06, 2013 6:44 am

Hi jbeuken,
I will try your recipe.
Thank you.
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Re: Abinit-7.2.1 compilation error with fftw3-mkl

Post by letuan » Wed Apr 10, 2013 12:14 pm

Dear jbeuken and everyones,
I repeated your recipe but unsuccessfully, the same error exists. In config.log I saw eventually the compilers are GNU, not icc and ifort.
So I added "FC=/usr/local/bin/mpif90 CC=icc CXX=icpc" for sure to the file build.ac. Then, I installed additionally fftw from fftw3-3.3.3.tar.gz (http://www.fftw.org). After that this "catastrophic error" dissapeared, but I ran into one more thing:

Code: Select all

checking for the size of a Fortran integer... configure: error: in `/home/letuan/Programs/abinit-7.2.1/fallbacks/sources/libxc-2.0.1':
configure: error: f90 program to find the size of a Fortran integer failed
See `config.log' for more details
make[2]: *** [stamps/libxc-config-stamp] Error 1
make[2]: Leaving directory `/home/letuan/Programs/abinit-7.2.1/fallbacks'
make[1]: [all-local] Error 2 (ignored)
Checking build of libxc fallback
test -e stamps/libxc-install-stamp
make[1]: *** [all-local] Error 1
make[1]: Leaving directory `/home/letuan/Programs/abinit-7.2.1/fallbacks'
make: *** [multi] Error 2

Is it because GNU compilers are default for Libxc while I was using icc and ifort?
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Re: Abinit-7.2.1 compilation error with fftw3-mkl

Post by Alain_Jacques » Thu Apr 11, 2013 3:36 pm

Hi letuan,

No, libxc should use the Intel compilers you specified although there is no problem to mix libraries compiled with gnu compilers and Intel compilers. Would you be so kind to post the /home/letuan/Programs/abinit-7.2.1/fallbacks/sources/libxc-2.0.1/config.log file.

Kind regards,

Alain
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Re: Abinit-7.2.1 compilation error with fftw3-mkl

Post by letuan » Fri Apr 12, 2013 8:55 am

Hi Alain,
Thank you for response. I think I've missed the step "export LD_LIBRARY_PATH...$LD_LIBRARY_PATH" for openMPI (but I already have these lines in .bash-profile, why there is no effect if I dis not issue the environment setting?)
Sorry, I will decsribe in more details in next mesage, because I am right now not with the computer.
Yours,
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Re: Abinit-7.2.1 compilation error with fftw3-mkl

Post by Alain_Jacques » Fri Apr 12, 2013 12:25 pm

Hi,

because in the configure script - libxc or the others - you'll find many tests checking the environment of your system by compiling and running tiny applets. Therefore the environment should be ready to run these programs and find the corresponding libraries if they live in "non standard" places. You'll probably find in the config.log, tests with -lmpi that fail although you have openmpi installed because the executable references something like libmpi.so without knowing where it is without the export. And then configure switches to another compiler.

On Linux, I would rather add exports LD_LIBRARY_PATH to .bashrc instead of .bash_profile but before adopting that, please understand the difference between a login and a non login shell. Another way - I would say a more definitive way - is to modify the system /etc/ldconfig ... but it can have side effects.

Kind regards,

Alain
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Re: Abinit-7.2.1 compilation error with fftw3-mkl

Post by letuan » Sun Apr 14, 2013 4:44 pm

Hi Alain and jbeyuken,
I spent a lot of time, even did instatlation from scratch (reinstall Linux, Intel C++ and Fortran compilers v.13.1, openmpi v. 1.6.4 and v. 1.7), but still faced with the "catastrophic error" as reported in the first message!!!
It seemed to be right the paths for environment variables and libraries for Intel Parallel Studio XE 2013 Update 3 and openmpi packages. I failed to used jbeuken's recipe, neither by direct typing in option for ./configure --opt=value with the key fclags-opt-66-wfs="-O1 ...". Even direct edit in Makefiles for all packages in abinit/src for replacement "-O3" by "-O1" cannot help. The error message is the same:

Code: Select all

0_10711

: catastrophic error: **Internal compiler error: internal abort** Please report this error along with the circumstances in which it occurred in a Software Problem Report.  Note: File and line given may not be explicit cause of this error.
compilation aborted for prep_fourwf.F90 (code 1)
make[4]: *** [prep_fourwf.o] Error 1

I have doubt on openmpi failure on my system, but even the clean installation of openmpi each time gives the warning during abinit's configuration like:

Code: Select all

 === Multicore architecture support                                         ===
 ==============================================================================

checking whether to enable OpenMP support... no
checking whether to build MPI code... yes
checking whether the C compiler supports MPI... no
checking whether the C++ compiler supports MPI... no
checking whether the Fortran Compiler supports MPI... yes
checking whether MPI is usable... no
configure: WARNING: MPI support is broken!
checking whether to build MPI I/O code... yes
checking whether to build MPI time tracing code... no
checking which level of MPI is supported by the Fortran compiler... 2
checking whether the MPI library supports MPI_CREATE_TYPE_STRUCT... yes
checking whether to activate GPU support... no

The config.log gives 0 return value.
{To Alain: due to the repeated environmental values, I got the previous errors with errors with LIBXC.. ,when I still did not go to the instalation of 66_wfs part. My the biggest concern is really this "catastrophic error for 66_wfs part!}
Pls, and anyone also, help me to fix the problem! Thank you .
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[Solved] Abinit-7.2.1 compilation error with fftw3-mkl

Post by letuan » Mon Apr 15, 2013 9:12 am

[Solved]
I have made some un-normal operation for compiling Abinit 7.2.1 + openmpi 1.7 + Intel Fortran compiler 13.1 with FFTW. The procedure is following:
1. Install Intel Parallel Studio XE 2013 Update 3. After compiling, I went into folder <instal-dir>/mkl/interfaces/fftw3xf, and issued the command

Code: Select all

make libintel64 compiler=intel
for building fftw library (I don't be sure in its neccessarity, but my configuration pointed on the library and I have to made it).
2. Install openmpi
3. First time, I issued ./configure command with key FCFLAGS="-O1" then "made". The recipe is not significantly different from jbeuken's one, but with the direction to Intel's fftw3 lib. Then, changing to FCFLAGS="-O2" for second configuration and final compiling. In the result, I still have the -O2 optimization level :P . This is my configuration recipe:

Code: Select all

./configure FC=/usr/local/bin/mpifort CC=icc CXX=icpc FCFLAGS="-O2" --with-dft-flavor=atompaw+bigdft+libxc --with-trio-flavor=netcdf+etsf_io+fox --with-linalg-flavor=mkl --with-linalg-libs="-L/opt/intel/mkl/lib/intel64/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lmkl_blas95_lp64 -lmkl_lapack95_lp64" --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/interfaces/fftw3xf/ -lfftw3xf_intel" --enable-mpi=yes --enable-mpi-io=yes --enable-optim=aggressive --with-fcflags-opt-66-wfs="-O1 -xHost -g -extend-source -vec-report0 -noaltparam -nofpscomp" --with-tardir=/home/letuan/Downloads/ABINIT/

But I cannot compile wannier90 fallback. The error message is "the C compiler can not create executable files". I put it away because I don't need in it for the moment.
Thank you very much for valuable help, jbeuken and Alain!!!
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Re: Abinit-7.2.1 compilation error with fftw3-mkl

Post by Alain_Jacques » Mon Apr 15, 2013 12:58 pm

Hi Letuan,

After compiling, I went into folder <instal-dir>/mkl/interfaces/fftw3xf, and issued the command

not necessary, not even recommended since this interface is flaky. Use fftw3 flavor by following Jean-Michel's recipe for the right interface libraries.

The catastrophic error is a bug in the compiler ... yeah shit happens. Check ulimit in order to be sure to have enough stack memory. In order to lower the optimization level on the offending source file, the right configuration option (if it works as a the command line version, not 100% sure about this - use a configuration file otherwise) is

Code: Select all

--with-fcflags-opt-66-wfs="-O1 -xHost -g -extend-source -vec-report0 -noaltparam -nofpscomp"


Kind regards,

Alain
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Re: [Solved]Abinit-7.2.1 compilation error with fftw3-mkl

Post by letuan » Wed Apr 17, 2013 2:33 am

Dear Alain,
OK. I switched to fftw-3.3.3 from www.fftw.org.
After issuing 'make check' my Abinit shown the same messages as for the Abinit v. 7.0.5.
Thank you again, Alain :)
Tuan
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Re: [Solved]Abinit-7.2.1 compilation error with fftw3-mkl

Post by pouillon » Mon Apr 22, 2013 12:23 pm

If you need to decrease optimizations for a specific directory, you'll have to use a config file. There is no --with-fcflags-opt-* option. See ~abinit/doc/build/config-template.ac for details.
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Re: [Solved]Abinit-7.2.1 compilation error with fftw3-mkl

Post by letuan » Mon Apr 22, 2013 3:51 pm

Thank you, Yann Puillon.
The only thing left for me at the moment is the message about lacking -lwannier path when I tried to compile with Wannier90 fallback.
Tuan.
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Re: [Solved]Abinit-7.2.1 compilation error with fftw3-mkl  [SOLVED]

Post by pouillon » Mon Apr 22, 2013 6:13 pm

If you don't need to perform calculations using Wannier functions, you may safely reconfigure without support for Wannier90. The following fits most situations perfectly well:

Code: Select all

../configure --with-dft-flavor="libxc" ... (your other options) ...
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Abinit-7.4.2 - compilation errors

Post by gryko » Sat Sep 28, 2013 6:07 pm

Hello,
I am trying to compile Abinit-7.4.2 on single CPU AMD 8-cores processor PC, running Fedora-18,
with mpi, and gfortran (mpif90). I installed libxc and atompaw, ACML, FFT3W (no problems,
all tests passed), the configuration runs fine, but during compilation I am getting
errors from this subroutine:

read_upf_pwscf_cpp.f90.

The error is in lines 49, 51, 62, for example, line 49:

if (matches("<PP_ "

and this is reported as a syntax error. The subroutine is in the folder 11_qespresso_ext.
I added missing )), but still the same error is reported.

Any suggestions, help?
Thank you,
Jan Gryko
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Re: Abinit-7.2.1 compilation error with fftw3-mkl

Post by pouillon » Wed Oct 02, 2013 12:11 pm

Add the following to your configure options:

Code: Select all

CPP="/lib/cpp" CPPFLAGS="-P -traditional-cpp" FPP="/lib/cpp" FPPFLAGS="-P -traditional-cpp"

If it doesn't work with /lib/cpp, try /usr/bin/cpp. And if it still doesn't work, find where the GNU C preprocessor is installed on your machine.
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