[gpaw-users] installation on CentOS 6, parallel version not built
Marcin Dulak
Marcin.Dulak at fysik.dtu.dk
Wed May 30 10:55:41 CEST 2012
Hi,
it looks that one needs to use the following define on rhel6:
define_macros.append(('_GNU_SOURCE', '1'))
Marcin
On 05/29/12 11:44, Misha Monder wrote:
> 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 <mailto:Marcin.Dulak at fysik.dtu.dk>
>
> ***********************************
>
>
--
***********************************
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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