[gpaw-users] installation on CentOS 6, parallel version not built

Tue May 29 11:44:18 CEST 2012

Hello Marcin,

Thank you for your note.

Appending the tail of build_ext.log below (not certain what the start point would be for what you are looking for). The full log file is attached as a file.

---------------------------
creating build/lib.linux-x86_64-2.6
gcc -pthread -shared build/temp.linux-x86_64-2.6/c/libxc.o build/temp.linux-x86_64-2.6/c/operators.o build/temp.linux-x86_64-2.6/c/hdf5.o build/temp.linux-x86_64-2.6/c/mlsqr.o build/temp.linux-x86_64-2.6/c/mpi.o build/temp.linux-x86_64-2.6/c/pw91.o build/temp.linux-x86_64-2.6/c/_gpaw.o build/temp.linux-x86_64-2.6/c/lfc2.o build/temp.linux-x86_64-2.6/c/xc.o build/temp.linux-x86_64-2.6/c/blas.o build/temp.linux-x86_64-2.6/c/lfc.o build/temp.linux-x86_64-2.6/c/pbe.o build/temp.linux-x86_64-2.6/c/spline.o build/temp.linux-x86_64-2.6/c/lcao.o build/temp.linux-x86_64-2.6/c/point_charges.o build/temp.linux-x86_64-2.6/c/plane_wave.o build/temp.linux-x86_64-2.6/c/transformers.o build/temp.linux-x86_64-2.6/c/ensemble_gga.o build/temp.linux-x86_64-2.6/c/vdw.o build/temp.linux-x86_64-2.6/c/cerf.o build/temp.linux-x86_64-2.6/c/localized_functions.o build/temp.linux-x86_64-2.6/c/utilities.o build/temp.linux-x86_64-2.6/c/rpbe.o build/temp.linux-x86_64-2.6/c/symmetry.o
 build/temp.linux-x86_64-2.6/c/wigner_seitz.o build/temp.linux-x86_64-2.6/c/bc.o build/temp.linux-x86_64-2.6/c/blacs.o build/temp.linux-x86_64-2.6/c/plt.o build/temp.linux-x86_64-2.6/c/lapack.o build/temp.linux-x86_64-2.6/c/bmgs/bmgs.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_xc_xlyp.o build/temp.linux-x86_64-2.6/c/libxc/src/hyb_gga_xc_x3lyp.o build/temp.linux-x86_64-2.6/c/libxc/src/mgga_c_m06l.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_c_p86.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_x_dk87.o build/temp.linux-x86_64-2.6/c/libxc/src/lca.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_x_rpbe.o build/temp.linux-x86_64-2.6/c/libxc/src/mgga_c_revtpss.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_x_am05.o build/temp.linux-x86_64-2.6/c/libxc/src/lda_c_xalpha.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_x_g96.o build/temp.linux-x86_64-2.6/c/libxc/src/hyb_gga_xc_o3lyp.o build/temp.linux-x86_64-2.6/c/libxc/src/mgga_c_tpss.o
 build/temp.linux-x86_64-2.6/c/libxc/src/gga_x_optx.o build/temp.linux-x86_64-2.6/c/libxc/src/lda_c_amgb.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_xc_lb.o build/temp.linux-x86_64-2.6/c/libxc/src/lda_c_vwn.o build/temp.linux-x86_64-2.6/c/libxc/src/lda_c_rpa.o build/temp.linux-x86_64-2.6/c/libxc/src/lda_c_pw.o build/temp.linux-x86_64-2.6/c/libxc/src/mgga_x_m06l.o build/temp.linux-x86_64-2.6/c/libxc/src/lda_c_hl.o build/temp.linux-x86_64-2.6/c/libxc/src/mgga_x_revtpss.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_x_pw91.o build/temp.linux-x86_64-2.6/c/libxc/src/hyb_gga_xc_b1wc.o build/temp.linux-x86_64-2.6/c/libxc/src/util.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_x_optb88.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_xc_hcth.o build/temp.linux-x86_64-2.6/c/libxc/src/mgga_x_tpss.o build/temp.linux-x86_64-2.6/c/libxc/src/hyb_gga_xc_b3pw91.o build/temp.linux-x86_64-2.6/c/libxc/src/special_functions.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_x_b88.o
 build/temp.linux-x86_64-2.6/c/libxc/src/mgga.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_x_pbe.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_x_wc.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_c_am05.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_x_pbea.o build/temp.linux-x86_64-2.6/c/libxc/src/lca_lch.o build/temp.linux-x86_64-2.6/c/libxc/src/hyb_gga_xc_b3p86.o build/temp.linux-x86_64-2.6/c/libxc/src/lda.o build/temp.linux-x86_64-2.6/c/libxc/src/hyb_gga_xc_b3lyp.o build/temp.linux-x86_64-2.6/c/libxc/src/functionals.o build/temp.linux-x86_64-2.6/c/libxc/src/lda_xc_teter93.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_x_mpbe.o build/temp.linux-x86_64-2.6/c/libxc/src/hyb_gga.o build/temp.linux-x86_64-2.6/c/libxc/src/gga.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_x_b86.o build/temp.linux-x86_64-2.6/c/libxc/src/hyb_gga_xc_pbeh.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_c_pbe.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_x_c09.o
 build/temp.linux-x86_64-2.6/c/libxc/src/gga_x_b86_mgc.o build/temp.linux-x86_64-2.6/c/libxc/src/lca_omc.o build/temp.linux-x86_64-2.6/c/libxc/src/lda_c_wigner.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_c_pw91.o build/temp.linux-x86_64-2.6/c/libxc/src/lda_c_pz.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_c_lyp.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_x_pw86.o build/temp.linux-x86_64-2.6/c/libxc/src/lda_x.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_perdew.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_xc_edf1.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_x_ft97.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_x_lg93.o -L/usr/lib64 -lblas -llapack -lpython2.6 -o build/lib.linux-x86_64-2.6/_gpaw.so
In file included from /usr/include/python2.6/Python.h:125,
                 from c/extensions.h:10,
                 from c/bc.c:12:
/usr/include/python2.6/modsupport.h:136: error: expected ‘)’ before ‘uid’
/usr/include/python2.6/modsupport.h:137: error: expected ‘)’ before ‘gid’
/usr/include/python2.6/modsupport.h:139: error: expected declaration specifiers or ‘...’ before ‘uid_t’
/usr/include/python2.6/modsupport.h:140: error: expected declaration specifiers or ‘...’ before ‘gid_t’
mpicc -DPARALLEL=1 -DGPAW_INTERPRETER=1 -Wall -std=c99 -I/usr/lib64/python2.6/site-packages/numpy/core/include -Ic/libxc -I/usr/include/python2.6 -I/usr/include/python2.6 -o build/temp.linux-x86_64-2.6/c/bc.o -c c/bc.c 
mpicc -o build/bin.linux-x86_64-2.6//gpaw-python build/temp.linux-x86_64-2.6/c/libxc.o build/temp.linux-x86_64-2.6/c/operators.o build/temp.linux-x86_64-2.6/c/hdf5.o build/temp.linux-x86_64-2.6/c/mlsqr.o build/temp.linux-x86_64-2.6/c/mpi.o build/temp.linux-x86_64-2.6/c/pw91.o build/temp.linux-x86_64-2.6/c/_gpaw.o build/temp.linux-x86_64-2.6/c/lfc2.o build/temp.linux-x86_64-2.6/c/xc.o build/temp.linux-x86_64-2.6/c/blas.o build/temp.linux-x86_64-2.6/c/lfc.o build/temp.linux-x86_64-2.6/c/pbe.o build/temp.linux-x86_64-2.6/c/spline.o build/temp.linux-x86_64-2.6/c/lcao.o build/temp.linux-x86_64-2.6/c/point_charges.o build/temp.linux-x86_64-2.6/c/plane_wave.o build/temp.linux-x86_64-2.6/c/transformers.o build/temp.linux-x86_64-2.6/c/ensemble_gga.o build/temp.linux-x86_64-2.6/c/vdw.o build/temp.linux-x86_64-2.6/c/cerf.o build/temp.linux-x86_64-2.6/c/localized_functions.o build/temp.linux-x86_64-2.6/c/utilities.o build/temp.linux-x86_64-2.6/c/rpbe.o
 build/temp.linux-x86_64-2.6/c/symmetry.o build/temp.linux-x86_64-2.6/c/wigner_seitz.o build/temp.linux-x86_64-2.6/c/bc.o build/temp.linux-x86_64-2.6/c/blacs.o build/temp.linux-x86_64-2.6/c/plt.o build/temp.linux-x86_64-2.6/c/lapack.o build/temp.linux-x86_64-2.6/c/bmgs/bmgs.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_xc_xlyp.o build/temp.linux-x86_64-2.6/c/libxc/src/hyb_gga_xc_x3lyp.o build/temp.linux-x86_64-2.6/c/libxc/src/mgga_c_m06l.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_c_p86.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_x_dk87.o build/temp.linux-x86_64-2.6/c/libxc/src/lca.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_x_rpbe.o build/temp.linux-x86_64-2.6/c/libxc/src/mgga_c_revtpss.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_x_am05.o build/temp.linux-x86_64-2.6/c/libxc/src/lda_c_xalpha.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_x_g96.o build/temp.linux-x86_64-2.6/c/libxc/src/hyb_gga_xc_o3lyp.o
 build/temp.linux-x86_64-2.6/c/libxc/src/mgga_c_tpss.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_x_optx.o build/temp.linux-x86_64-2.6/c/libxc/src/lda_c_amgb.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_xc_lb.o build/temp.linux-x86_64-2.6/c/libxc/src/lda_c_vwn.o build/temp.linux-x86_64-2.6/c/libxc/src/lda_c_rpa.o build/temp.linux-x86_64-2.6/c/libxc/src/lda_c_pw.o build/temp.linux-x86_64-2.6/c/libxc/src/mgga_x_m06l.o build/temp.linux-x86_64-2.6/c/libxc/src/lda_c_hl.o build/temp.linux-x86_64-2.6/c/libxc/src/mgga_x_revtpss.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_x_pw91.o build/temp.linux-x86_64-2.6/c/libxc/src/hyb_gga_xc_b1wc.o build/temp.linux-x86_64-2.6/c/libxc/src/util.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_x_optb88.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_xc_hcth.o build/temp.linux-x86_64-2.6/c/libxc/src/mgga_x_tpss.o build/temp.linux-x86_64-2.6/c/libxc/src/hyb_gga_xc_b3pw91.o
 build/temp.linux-x86_64-2.6/c/libxc/src/special_functions.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_x_b88.o build/temp.linux-x86_64-2.6/c/libxc/src/mgga.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_x_pbe.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_x_wc.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_c_am05.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_x_pbea.o build/temp.linux-x86_64-2.6/c/libxc/src/lca_lch.o build/temp.linux-x86_64-2.6/c/libxc/src/hyb_gga_xc_b3p86.o build/temp.linux-x86_64-2.6/c/libxc/src/lda.o build/temp.linux-x86_64-2.6/c/libxc/src/hyb_gga_xc_b3lyp.o build/temp.linux-x86_64-2.6/c/libxc/src/functionals.o build/temp.linux-x86_64-2.6/c/libxc/src/lda_xc_teter93.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_x_mpbe.o build/temp.linux-x86_64-2.6/c/libxc/src/hyb_gga.o build/temp.linux-x86_64-2.6/c/libxc/src/gga.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_x_b86.o build/temp.linux-x86_64-2.6/c/libxc/src/hyb_gga_xc_pbeh.o
 build/temp.linux-x86_64-2.6/c/libxc/src/gga_c_pbe.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_x_c09.o build/temp.linux-x86_64-2.6/c/li/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../lib64/crt1.o: In function `_start':
(.text+0x20): undefined reference to `main'
collect2: ld returned 1 exit status
bxc/src/gga_x_b86_mgc.o build/temp.linux-x86_64-2.6/c/libxc/src/lca_omc.o build/temp.linux-x86_64-2.6/c/libxc/src/lda_c_wigner.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_c_pw91.o build/temp.linux-x86_64-2.6/c/libxc/src/lda_c_pz.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_c_lyp.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_x_pw86.o build/temp.linux-x86_64-2.6/c/libxc/src/lda_x.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_perdew.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_xc_edf1.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_x_ft97.o build/temp.linux-x86_64-2.6/c/libxc/src/gga_x_lg93.o  -L/usr/lib64/python2.6/config -lblas -llapack -lpython2.6 -lpthread -ldl  -lutil -lm  -L/usr/lib6464 -Xlinker -export-dynamic

* Using standard lapack
* Architecture: linux-x86_64
* Building a custom interpreter
* linking FAILED!  Only serial version of code will work.

------------------------------------

________________________________
 From: Marcin Dulak <Marcin.Dulak at fysik.dtu.dk>
To: Misha Monder <misha_monder at yahoo.com> 
Cc: GPAW Users List <gpaw-users at listserv.fysik.dtu.dk> 
Sent: Tuesday, May 29, 2012 1:51:32 PM
Subject: Re: [gpaw-users] installation on CentOS 6, parallel version not built

Hi,

On 05/28/12 20:27, Misha Monder wrote: 
Hello all,
>
>
>I am trying to install GPAW on my CentOS 6.2, dual processor intel xeon machine.
>
>
>
>I followed the basic directions at https://wiki.fysik.dtu.dk/gpaw/install/Linux/CentOS.html#centos 
>
>However, although most tests work in serial mode, the parallel version is missing. I have tried using openmpi 1.5.3 and mpich2 1.2.1 (using modules) without success. I get the following at the end of the install.log: "* Only a serial version of gpaw was built!"
>
>
>mpicc -v gives me the expected version of mpi. 
>
>
>
>I also tried doing a developers installation. The problem above remains and I cannot seem to build the parallel version of gpaw. The installation script seems to find mpicc (have tried with openmpi 1.5.3 and mpich2 1.2.1) but I get a "* linking FAILED!  Only serial version of code will work." message when building the C extensions. 
>
please perform https://wiki.fysik.dtu.dk/gpaw/devel/developer_installation.html#developer-installation
and post the tail of build_ext.log (the linking errors).

Best regards,

Marcin

>
>I am using standard lapack/blas so far. 
>
>
>
>I would be very grateful for any suggestions.
>
>
>Thanks,
>Misha
>
>

-- 
*********************************** Marcin Dulak
Technical University of Denmark
Department of Physics
Building 307, Room 229
DK-2800 Kongens Lyngby
Denmark
Tel.: (+45) 4525 3157
Fax.: (+45) 4593 2399
email: Marcin.Dulak at fysik.dtu.dk *********************************** 
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