abinit installation error in make

mina · Post by **mina** » Tue Jan 22, 2013 12:05 pm

Hello,
Dear all users i wana to install abinit7.0.5 on my linux debian.i could get it and did command ./configure it was complete but when i use command make i have an error:
checking for Fortran flag to compile .f90 files... unknown
configure: error: Fortran could not compile .f90 files
make[3]: *** [stamps/libxc-config-stamp] Error 1
make[3]: Leaving directory `/home/mina/abinit-7.0.5/fallbacks'
make[2]: [all-local] Error 2 (ignored)
Checking build of libxc fallback
test -e stamps/libxc-install-stamp
make[2]: *** [all-local] Error 1
make[2]: Leaving directory `/home/mina/abinit-7.0.5/fallbacks'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/mina/abinit-7.0.5'
make: *** [all] Error 2
i have gfortran-4.4 on my pc and gcc too.
Would you please help me to install abinit?
Best regards.
Mina.

Post by **pouillon** » Tue Jan 22, 2013 12:50 pm

Please attach the following file to your previous post: <your_abinit_build_dir>/fallbacks/sources/libxc-1.1.0.1/config.log, so that we can diagnose the problem correctly.

mina · Post by **mina** » Wed Jan 23, 2013 7:35 am

Dear pouillon,
Thankyou for your help.i have attached that file for you.
Best regards.
Mina.

Alain_Jacques · Post by **Alain_Jacques** » Wed Jan 23, 2013 2:40 pm

Hi Mina,

libxc configure picks up f77 as the working fortran compiler and it doesn't work as expected. I assume that you have gfortran installed on your system and is in the PATH i.e. it is returned when you invoke "which gfortran". Either remove of the offending f77 or specify FC=gfortran during Abinit configuration step.

Kind regards,

Alain

letuan · Post by **letuan** » Fri Jan 25, 2013 4:20 pm

Hi all and Alain,
I'm a newcomer and I have the same error as mina wrote, despite on that the compilation has been made by ordinary user or by root:

make[4]: Leaving directory `/home/letuan/abinit-7.0.5/tests'
v3/tmp-test_Linux_20130123/report:Case_30 failed (too many erroneous lines : 8 , accepted 6 )
v3/tmp-test_Linux_20130123/report:Case_87 failed (too many erroneous lines : 4 , accepted 3 )
v3/tmp-test_Linux_20130124/report:Case_30 failed (too many erroneous lines : 8 , accepted 6 )
v3/tmp-test_Linux_20130124/report:Case_87 failed (too many erroneous lines : 4 , accepted 3 )
make[3]: *** [check-local] Error 1
make[3]: Leaving directory `/home/letuan/abinit-7.0.5/tests'
make[2]: *** [check-am] Error 2
make[2]: Leaving directory `/home/letuan/abinit-7.0.5/tests'
make[1]: *** [check-recursive] Error 1
make[1]: Leaving directory `/home/letuan/abinit-7.0.5/tests'
make: *** [check-recursive] Error 1

I use Intel compilers 13.0 from non-commercial Intel Parallel Studio XE 2013 suite (installed in /opt/Intel) on SuSE Enterprise Server 11 SP2 and OpenMPI-1.6.3 (in /usr/local). My hardware is IBM X3550, 2 Xeon x 4 core, but with only 8 GB RAM.
The configuration was made by :
./configure FC=/usr/local/bin/mpif90 CC=icc CXX=icpc FCFLAGS='-O2' --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 --enable-optim=aggressive
Would you help me to resolve this error?
Thank you a lot

mina · Post by **mina** » Sat Jan 26, 2013 11:13 am

Dear Alain,
Thanks for your help,abinit installed on my pc.
Best regards.
Mina

Alain_Jacques · Post by **Alain_Jacques** » Sun Jan 27, 2013 5:12 pm

Hi Letuan,

Not really the "same" error message :-)

Anyway I assume you succeeded in compiling abinit (?) - you should have an executable abinit binary in src/98_main - and have errors returned when performing the tests (?) I cannot guess what's wrong in v3t30 and v3t87. Look at the corresponding t30.err and t87.err for error messages and analyze diff.t30 and diff.t87 for clues. And please attach t30.out and t87.out to your post.

I see several cranky options in your configuration line but I cannot say if they are toxic - would you be so kind to add config.h and src/98_main/Makefile too.

Kind regards,

Alain

letuan · Post by **letuan** » Tue Jan 29, 2013 3:00 pm

Hi Alain,
There are my files. Sorry, because this forum permits to attach no more than 3 files in a message, I print the file t30.out to the message's body.
I am wondering, if I switch to openSUSE 12.2 from SLES 11 SP2, the problem may disappear because of newer libraries?
I compiled abinit and can call it for small testing calculation. In comparison with my friend's output (he works on well configured and working system), the results are different only at (-9 to -10 order) numbers.
Thank you for attention and help
Tuan

Code: Select all

,3c2,3
< .Version 7.0.5 of ABINIT 
< .(MPI version, prepared for a x86_64_linux_intel13.0 computer) 
---
> .Version 7.0.0 of ABINIT 
> .(MPI version, prepared for a x86_64_linux_gnu4.4 computer) 
17,18c17,18
< .Starting date : Thu 24 Jan 2013.
< - ( at 19h41 )
---
> .Starting date : Sat 25 Aug 2012.
> - ( at 14h11 )
20c20
< - input  file    -> /home/letuan/abinit-7.0.5/tests/v3/Input/t30.in
---
> - input  file    -> /home/gonze/ABINIT/ABINITv7.0.0/trunk/7.0.0-training/tests/v3/Input/t30.in
411,412c411,412
< - pspini: atom type   1  psp file is /home/letuan/abinit-7.0.5/tests/Psps_for_tests/14si.pspnc
< - pspatm: opening atomic psp file    /home/letuan/abinit-7.0.5/tests/Psps_for_tests/14si.pspnc
---
> - pspini: atom type   1  psp file is /home/gonze/ABINIT/ABINITv7.0.0/trunk/7.0.0-training/tests/Psps_for_tests/14si.pspnc
> - pspatm: opening atomic psp file    /home/gonze/ABINIT/ABINITv7.0.0/trunk/7.0.0-training/tests/Psps_for_tests/14si.pspnc
441,449c441,449
<  ETOT  2  -8.8589846693226    -4.798E-03 1.144E-07 1.283E-01
<  ETOT  3  -8.8590990326196    -1.144E-04 5.091E-06 2.595E-02
<  ETOT  4  -8.8591133676399    -1.434E-05 7.921E-07 3.412E-03
<  ETOT  5  -8.8591154391855    -2.072E-06 1.793E-07 2.497E-04
<  ETOT  6  -8.8591156647355    -2.256E-07 1.329E-08 5.539E-06
<  ETOT  7  -8.8591156691153    -4.380E-09 4.012E-10 1.647E-08
<  ETOT  8  -8.8591156691162    -9.130E-13 3.324E-14 1.658E-08
<  ETOT  9  -8.8591156691238    -7.546E-12 5.576E-13 1.375E-09
<  ETOT 10  -8.8591156691250    -1.208E-12 9.535E-14 4.320E-12
---
>  ETOT  2  -8.8589846693224    -4.798E-03 1.144E-07 1.283E-01
>  ETOT  3  -8.8590990326194    -1.144E-04 5.091E-06 2.595E-02
>  ETOT  4  -8.8591133676398    -1.434E-05 7.921E-07 3.412E-03
>  ETOT  5  -8.8591154391854    -2.072E-06 1.793E-07 2.497E-04
>  ETOT  6  -8.8591156647354    -2.255E-07 1.329E-08 5.539E-06
>  ETOT  7  -8.8591156691152    -4.380E-09 4.012E-10 1.647E-08
>  ETOT  8  -8.8591156691161    -8.953E-13 3.324E-14 1.658E-08
>  ETOT  9  -8.8591156691237    -7.624E-12 5.576E-13 1.375E-09
>  ETOT 10  -8.8591156691248    -1.098E-12 9.535E-14 4.320E-12
534,536c534,536
<  rms dE/dt=  4.2940E-30; max dE/dt=  6.3109E-30; dE/dt below (all hartree)
<     1       0.000000000000      0.000000000000      0.000000000000
<     2      -0.000000000000     -0.000000000000     -0.000000000000
---
>  rms dE/dt=  2.8483E-30; max dE/dt=  4.2073E-30; dE/dt below (all hartree)
>     1      -0.000000000000      0.000000000000      0.000000000000
>     2      -0.000000000000     -0.000000000000      0.000000000000
543,545c543,545
<     1     -0.00000000000000     0.00000000000000    -0.00000000000000
<     2      0.00000000000000    -0.00000000000000     0.00000000000000
<  frms,max,avg= 5.1308026E-31 7.1831237E-31   0.000E+00  0.000E+00  0.000E+00 h/b
---
>     1      0.00000000000000     0.00000000000000    -0.00000000000000
>     2     -0.00000000000000    -0.00000000000000     0.00000000000000
>  frms,max,avg= 1.9649478E-31 3.0784816E-31   0.000E+00  0.000E+00  0.000E+00 h/b
548,550c548,550
<     1     -0.00000000000000     0.00000000000000    -0.00000000000000
<     2      0.00000000000000    -0.00000000000000     0.00000000000000
<  frms,max,avg= 2.6383646E-29 3.6937104E-29   0.000E+00  0.000E+00  0.000E+00 e/A
---
>     1      0.00000000000000     0.00000000000000    -0.00000000000000
>     2     -0.00000000000000    -0.00000000000000     0.00000000000000
>  frms,max,avg= 1.0104167E-29 1.5830187E-29   0.000E+00  0.000E+00  0.000E+00 e/A
580,582c580,582
<     Kinetic energy  =  3.01475598950716E+00
<     Hartree energy  =  5.49241354548001E-01
<     XC energy       = -3.53650872677963E+00
---
>     Kinetic energy  =  3.01475598950717E+00
>     Hartree energy  =  5.49241354548012E-01
>     XC energy       = -3.53650872677964E+00
584c584
<     PspCore energy  =  8.52154029740039E-02
---
>     PspCore energy  =  8.52154029741278E-02
586,587c586,587
<     NL   psp  energy=  1.91834831974219E+00
<     >>>>>>>>> Etotal= -8.85911566912499E+00
---
>     NL   psp  energy=  1.91834831974220E+00
>     >>>>>>>>> Etotal= -8.85911566912484E+00
590c590
<     Total energy(eV)= -2.41068797132701E+02 ; Band energy (Ha)=   2.3034836898E-01
---
>     Total energy(eV)= -2.41068797132697E+02 ; Band energy (Ha)=   2.3034836898E-01
618c618
< .Using single precision arithmetic ; gwpc =  4
---
> .Using double precision arithmetic ; gwpc =  8
628,629c628,629
< - pspini: atom type   1  psp file is /home/letuan/abinit-7.0.5/tests/Psps_for_tests/14si.pspnc
< - pspatm: opening atomic psp file    /home/letuan/abinit-7.0.5/tests/Psps_for_tests/14si.pspnc
---
> - pspini: atom type   1  psp file is /home/gonze/ABINIT/ABINITv7.0.0/trunk/7.0.0-training/tests/Psps_for_tests/14si.pspnc
> - pspatm: opening atomic psp file    /home/gonze/ABINIT/ABINITv7.0.0/trunk/7.0.0-training/tests/Psps_for_tests/14si.pspnc
686c686
<  max sum_G |a(n,k,G)| =  0.999938
---
>  max sum_G |a(n,k,G)| =  0.999937
710c710
<     2   0.000 -11.936   0.000  -0.141  -0.000  -0.141  -0.000  -0.141  -0.000
---
>     2   0.000 -11.936  -0.000  -0.141  -0.000  -0.141   0.000  -0.141  -0.000
718,719c718,719
<     2   0.000  -3.267  -0.000   0.073  -0.000   0.073  -0.000   0.073  -0.000
<        -0.000   0.000  -1.146   0.000  -0.063   0.000  -0.063  -0.000  -0.063
---
>     2   0.000  -3.267   0.000   0.073   0.000   0.073   0.000   0.073   0.000
>        -0.000  -0.000  -1.146  -0.000  -0.063  -0.000  -0.063   0.000  -0.063
756,757c756,757
<     2  -1.674  -7.358  -0.000   0.247   0.000   0.247   0.000   0.247   0.000
<         1.674  -0.000  -3.856  -0.000   0.226   0.000   0.226  -0.000   0.226
---
>     2  -1.674  -7.358  -0.000   0.247  -0.000   0.247  -0.000   0.247   0.000
>         1.674  -0.000  -3.856   0.000   0.226   0.000   0.226   0.000   0.226
764,765c764,765
<     2  -0.535  -1.888   0.000   0.074   0.000   0.074  -0.000   0.074  -0.000
<         0.535  -0.000  -0.834  -0.000   0.001   0.000   0.001   0.000   0.001
---
>     2  -0.535  -1.888   0.000   0.074  -0.000   0.074   0.000   0.074   0.000
>         0.535  -0.000  -0.834  -0.000   0.001  -0.000   0.001   0.000   0.001
775,776c775,776
<     1 -14.007   0.177  -2.094  -2.094   0.177  -2.242  -2.242  -2.242  -2.242
<         0.000   0.177   2.094  -2.094  -0.177  -2.242   2.242  -2.242   2.242
---
>     1 -14.006   0.177  -2.094  -2.094   0.177  -2.242  -2.242  -2.242  -2.242
>        -0.000   0.177   2.094  -2.094  -0.177  -2.242   2.242  -2.242   2.242
778,779c778,779
<     2   0.177 -14.808   0.000  -0.156  -0.000   0.850  -0.000   0.850  -0.000
<        -0.177   0.000  -3.241   0.000  -1.772  -0.000  -0.040   0.000  -0.040
---
>     2   0.177 -14.808   0.000  -0.156  -0.000   0.850  -0.000   0.850   0.000
>        -0.177   0.000  -3.241   0.000  -1.773   0.000  -0.040  -0.000  -0.040
784c784
<         0.000   0.175   0.475  -0.475  -0.175  -0.384   0.384  -0.384   0.384
---
>        -0.000   0.175   0.475  -0.475  -0.175  -0.384   0.384  -0.384   0.384
786,787c786,787
<     2   0.175  -3.403   0.000   0.033  -0.000   0.111   0.000   0.111   0.000
<        -0.175   0.000  -0.838  -0.000  -0.196  -0.000  -0.079   0.000  -0.079
---
>     2   0.175  -3.403   0.000   0.033  -0.000   0.111  -0.000   0.111  -0.000
>        -0.175   0.000  -0.838  -0.000  -0.196  -0.000  -0.079  -0.000  -0.079
798c798
<         0.000  -0.278   2.141  -0.278   2.141  -2.141   0.278  -2.141   0.278
---
>        -0.000  -0.278   2.141  -0.278   2.141  -2.141   0.278  -2.141   0.278
800,801c800,801
<     2  -0.278 -13.485   0.000   2.418  -0.000  -0.394   0.000  -0.394   0.000
<         0.278  -0.000  -3.435   0.000  -0.216  -0.000  -0.359  -0.000  -0.359
---
>     2  -0.278 -13.485   0.000   2.418   0.000  -0.394  -0.000  -0.394   0.000
>         0.278   0.000  -3.435  -0.000  -0.216  -0.000  -0.359  -0.000  -0.359
806c806
<         0.000   0.022   0.361   0.022   0.361  -0.361  -0.022  -0.361  -0.022
---
>        -0.000   0.022   0.361   0.022   0.361  -0.361  -0.022  -0.361  -0.022
808,809c808,809
<     2   0.022  -3.376   0.000   0.270  -0.000   0.023   0.000   0.023  -0.000
<        -0.022  -0.000  -0.925   0.000  -0.029  -0.000  -0.119  -0.000  -0.119
---
>     2   0.022  -3.376   0.000   0.270   0.000   0.023   0.000   0.023  -0.000
>        -0.022   0.000  -0.925  -0.000  -0.029   0.000  -0.119   0.000  -0.119
822,823c822,823
<     2  -1.582 -16.040   0.000  -0.099   0.000   1.854   0.000  -0.240   0.000
<         1.582   0.000  -2.310   0.000   0.000   0.000   0.109  -0.000  -0.000
---
>     2  -1.582 -16.040   0.000  -0.099   0.000   1.854   0.000  -0.240  -0.000
>         1.582   0.000  -2.310  -0.000   0.000   0.000   0.109   0.000  -0.000
828c828
<         0.000  -0.170   0.504  -0.528   0.482  -0.482   0.528  -0.504   0.170
---
>        -0.000  -0.170   0.504  -0.528   0.482  -0.482   0.528  -0.504   0.170
830,831c830,831
<     2  -0.170  -3.309  -0.000  -0.063  -0.000   0.175  -0.000   0.028  -0.000
<         0.170  -0.000  -0.470  -0.000  -0.000  -0.000  -0.033   0.000   0.000
---
>     2  -0.170  -3.309  -0.000  -0.063  -0.000   0.175  -0.000   0.028   0.000
>         0.170   0.000  -0.470  -0.000  -0.000   0.000  -0.033   0.000  -0.000
842c842
<        -0.000  -1.450   2.144  -2.144   1.450  -1.450   2.144  -2.144   1.450
---
>         0.000  -1.450   2.144  -2.144   1.450  -1.450   2.144  -2.144   1.450
844,845c844,845
<     2  -1.450 -13.835  -0.000  -0.011   0.000   3.405   0.000  -0.011  -0.000
<         1.450   0.000  -1.973  -0.000  -0.000   0.000  -0.135   0.000   0.000
---
>     2  -1.450 -13.836  -0.000  -0.011  -0.000   3.405  -0.000  -0.011   0.000
>         1.450  -0.000  -1.973  -0.000   0.000  -0.000  -0.135   0.000   0.000
852,853c852,853
<     2  -0.303  -3.399   0.000   0.016  -0.000   0.386  -0.000   0.016   0.000
<         0.303   0.000  -0.520   0.000   0.000  -0.000  -0.014  -0.000  -0.000
---
>     2  -0.303  -3.399  -0.000   0.016  -0.000   0.386   0.000   0.016  -0.000
>         0.303   0.000  -0.520   0.000  -0.000   0.000  -0.014   0.000  -0.000
874c874
< .Using single precision arithmetic ; gwpc =  4
---
> .Using double precision arithmetic ; gwpc =  8
922c922
<  max sum_G |a(n,k,G)| =  0.999938
---
>  max sum_G |a(n,k,G)| =  0.999937
998c998
< .Using single precision arithmetic ; gwpc =  4
---
> .Using double precision arithmetic ; gwpc =  8
1046c1046
<  max sum_G |a(n,k,G)| =  0.999938
---
>  max sum_G |a(n,k,G)| =  0.999937
1122c1122
< .Using single precision arithmetic ; gwpc =  4
---
> .Using double precision arithmetic ; gwpc =  8
1170c1170
<  max sum_G |a(n,k,G)| =  0.999938
---
>  max sum_G |a(n,k,G)| =  0.999937
1246c1246
< .Using single precision arithmetic ; gwpc =  4
---
> .Using double precision arithmetic ; gwpc =  8
1294c1294
<  max sum_G |a(n,k,G)| =  0.999938
---
>  max sum_G |a(n,k,G)| =  0.999937
1400,1401c1400,1401
<             fcart1    -7.1831236898E-31  1.0261605271E-31 -5.1308026356E-31
<                        7.1831236898E-31 -1.0261605271E-31  5.1308026356E-31
---
>             fcart1     1.0261605271E-31  1.0261605271E-31 -3.0784815814E-31
>                       -1.0261605271E-31 -1.0261605271E-31  3.0784815814E-31
1549c1549
<            strten1     9.5096202565E-05  9.5096202565E-05  9.5096202565E-05
---
>            strten1     9.5096202564E-05  9.5096202564E-05  9.5096202564E-05
1696c1696
< - Proc.   0 individual time (sec): cpu=          5.3  wall=          5.3
---
> - Proc.   0 individual time (sec): cpu=          3.5  wall=          3.5
1701,1702c1701,1702
< .Delivered   37 WARNINGs and  27 COMMENTs to log file.
< +Overall time at end (sec) : cpu=          5.3  wall=          5.3
---
> .Delivered   32 WARNINGs and  27 COMMENTs to log file.
> +Overall time at end (sec) : cpu=          3.8  wall=          3.8

Alain_Jacques · Post by **Alain_Jacques** » Tue Jan 29, 2013 5:41 pm

Hi Tuan,

I had a look on your t30 and t87 output ... nothing toxic, only small differences due to single/double precision gw calculations. So I assume you have a working abinit binary.

From the config.h and Makefile, I see that you use the internal FFT library - you have MKL installed on your system, it is more efficient so it would be a pity not to use it.

Concerning the error messages, I have no clue where they come from. The procedure to compile and test abinit consists of the following steps:

If you follow that recipe, make shouldn't return error messages during the tests.

Kind regards,

Alain

letuan · Post by **letuan** » Tue Jan 29, 2013 6:14 pm

Thank you for prompt response, Alain.
I gues I may use already MKL ? Please, show me more details in configuration for being sure that MKL would be in use! I am intend to use MKL, but I don't know how to check.
I made some tests in test subdirectory and it seems to be normal. The error message appears at the end of "make check" procedure. I will do tests again as you advised.
Again, thank you very much, Alain.

letuan · Post by **letuan** » Fri Feb 01, 2013 4:43 am

Dear Alain,
The running "make tests_acc4" seems to not show any error message.
Thank you for help.
Tuan

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