Installation of GPAW fails

[ipsecog]

I'm trying to install GPAW in ATK 10.8 on a Linux system, but I get a lot of weird error messages. I separated stdout and stderr to see what's going on, I'm just showing the end, where it goes wrong:

STDOUT

Writing ../../lib/python2.6/site-packages/gpaw-0.6.5147-py2.6.egg-info
mpicc -DPARALLEL=1 -DGPAW_INTERPRETER=1 -Wall -std=c99 -I/home/anders/QuantumWise/atk-10.8.0/atkpython/lib/python2.6/site-packages/numpy/core/include -Ic/libxc -I/home/quantum/quantumnotes/qw-control/quantumconnect/trunk/external-libs/build/include/python2.6 -I/home/quantum/quantumnotes/qw-control/quantumconnect/trunk/external-libs/build/include/python2.6 -o build/temp.linux-i686-2.6/c/bc.o -c c/bc.c
mpicc -o build/bin.linux-i686-2.6//gpaw-python build/temp.linux-i686-2.6/c/xc.o build/temp.linux-i686-2.6/c/libxc.o build/temp.linux-i686-2.6/c/pbe.o build/temp.linux-i686-2.6/c/point_charges.o build/temp.linux-i686-2.6/c/spline.o build/temp.linux-i686-2.6/c/vasiliev02prb.o build/temp.linux-i686-2.6/c/pw91.o build/temp.linux-i686-2.6/c/wigner_seitz.o build/temp.linux-i686-2.6/c/compiled_WITH_SL.o build/temp.linux-i686-2.6/c/blas.o build/temp.linux-i686-2.6/c/d2Excdn2.o build/temp.linux-i686-2.6/c/rpbe.o build/temp.linux-i686-2.6/c/ensemble_gga.o build/temp.linux-i686-2.6/c/tpss.o build/temp.linux-i686-2.6/c/_gpaw.o build/temp.linux-i686-2.6/c/utilities.o build/temp.linux-i686-2.6/c/tpss_ec.o build/temp.linux-i686-2.6/c/mpi.o build/temp.linux-i686-2.6/c/localized_functions.o build/temp.linux-i686-2.6/c/lb94.o build/temp.linux-i686-2.6/c/tpss_ex.o build/temp.linux-i686-2.6/c/bc.o build/temp.linux-i686-2.6/c/plt.o build/temp.linux-i686-2.6/c/transformers.o build/temp.linux-i686-2.6/c/mgga.o build/temp.linux-i686-2.6/c/lcao.o build/temp.linux-i686-2.6/c/lfc.o build/temp.linux-i686-2.6/c/operators.o build/temp.linux-i686-2.6/c/blacs.o build/temp.linux-i686-2.6/c/lapack.o build/temp.linux-i686-2.6/c/vdw.o build/temp.linux-i686-2.6/c/mlsqr.o build/temp.linux-i686-2.6/c/bmgs/bmgs.o build/temp.linux-i686-2.6/c/libxc/src/gga_c_lyp.o build/temp.linux-i686-2.6/c/libxc/src/gga_x_rpbe.o build/temp.linux-i686-2.6/c/libxc/src/lda.o build/temp.linux-i686-2.6/c/libxc/src/lca_omc.o build/temp.linux-i686-2.6/c/libxc/src/gga.o build/temp.linux-i686-2.6/c/libxc/src/gga_c_p86.o build/temp.linux-i686-2.6/c/libxc/src/lda_x.o build/temp.linux-i686-2.6/c/libxc/src/gga_xc_xlyp.o build/temp.linux-i686-2.6/c/libxc/src/gga_x_am05.o build/temp.linux-i686-2.6/c/libxc/src/lda_xc_teter93.o build/temp.linux-i686-2.6/c/libxc/src/gga_x_optx.o build/temp.linux-i686-2.6/c/libxc/src/lda_c_hl.o build/temp.linux-i686-2.6/c/libxc/src/hyb_gga_xc_o3lyp.o build/temp.linux-i686-2.6/c/libxc/src/hyb_gga_xc_pbeh.o build/temp.linux-i686-2.6/c/libxc/src/mgga_c_m06l.o build/temp.linux-i686-2.6/c/libxc/src/functionals.o build/temp.linux-i686-2.6/c/libxc/src/hyb_gga_xc_b1wc.o build/temp.linux-i686-2.6/c/libxc/src/lca_lch.o build/temp.linux-i686-2.6/c/libxc/src/gga_xc_edf1.o build/temp.linux-i686-2.6/c/libxc/src/gga_x_pw86.o build/temp.linux-i686-2.6/c/libxc/src/gga_x_ft97.o build/temp.linux-i686-2.6/c/libxc/src/hyb_gga.o build/temp.linux-i686-2.6/c/libxc/src/lda_c_amgb.o build/temp.linux-i686-2.6/c/libxc/src/util.o build/temp.linux-i686-2.6/c/libxc/src/gga_c_pw91.o build/temp.linux-i686-2.6/c/libxc/src/gga_x_g96.o build/temp.linux-i686-2.6/c/libxc/src/hyb_gga_xc_b3p86.o build/temp.linux-i686-2.6/c/libxc/src/gga_x_pw91.o build/temp.linux-i686-2.6/c/libxc/src/gga_xc_lb.o build/temp.linux-i686-2.6/c/libxc/src/gga_c_pbe.o build/temp.linux-i686-2.6/c/libxc/src/gga_x_mpbe.o build/temp.linux-i686-2.6/c/libxc/src/lda_c_rpa.o build/temp.linux-i686-2.6/c/libxc/src/hyb_gga_xc_b3lyp.o build/temp.linux-i686-2.6/c/libxc/src/gga_xc_hcth.o build/temp.linux-i686-2.6/c/libxc/src/gga_x_wc.o build/temp.linux-i686-2.6/c/libxc/src/lda_c_wigner.o build/temp.linux-i686-2.6/c/libxc/src/gga_x_b88.o build/temp.linux-i686-2.6/c/libxc/src/gga_x_lg93.o build/temp.linux-i686-2.6/c/libxc/src/gga_x_pbe.o build/temp.linux-i686-2.6/c/libxc/src/mgga_x_m06l.o build/temp.linux-i686-2.6/c/libxc/src/gga_x_pbea.o build/temp.linux-i686-2.6/c/libxc/src/hyb_gga_xc_x3lyp.o build/temp.linux-i686-2.6/c/libxc/src/gga_x_dk87.o build/temp.linux-i686-2.6/c/libxc/src/special_functions.o build/temp.linux-i686-2.6/c/libxc/src/lda_c_pw.o build/temp.linux-i686-2.6/c/libxc/src/mgga.o build/temp.linux-i686-2.6/c/libxc/src/mgga_c_tpss.o build/temp.linux-i686-2.6/c/libxc/src/gga_c_am05.o build/temp.linux-i686-2.6/c/libxc/src/gga_x_b86.o build/temp.linux-i686-2.6/c/libxc/src/mgga_x_tpss.o build/temp.linux-i686-2.6/c/libxc/src/gga_perdew.o build/temp.linux-i686-2.6/c/libxc/src/lda_c_xalpha.o build/temp.linux-i686-2.6/c/libxc/src/hyb_gga_xc_b3pw91.o build/temp.linux-i686-2.6/c/libxc/src/lda_c_vwn.o build/temp.linux-i686-2.6/c/libxc/src/lca.o build/temp.linux-i686-2.6/c/libxc/src/gga_x_b86_mgc.o build/temp.linux-i686-2.6/c/libxc/src/lda_c_pz.o  -L. -L/home/quantum/quantumnotes/qw-control/quantumconnect/trunk/external-libs/build/lib/python2.6/config -lmkl_intel -lmkl_intel_thread -lmkl_lapack -lmkl_def -lmkl_core -liomp5 -lpython2.6 -lpthread -ldl  -lutil -lm  -Xlinker -export-dynamic

STDERR

/opt/QuantumWise/atk-10.8.0/atkpython/lib/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:871: error: expected specifier-qualifier-list before 'PyObject_HEAD'
/opt/QuantumWise/atk-10.8.0/atkpython/lib/python2.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:1084: error: expected specifier-qualifier-list before 'npy_intp'
/usr/lib/gcc/i486-linux-gnu/4.4.3/../../../../lib/crt1.o: In function `_start':
(.text+0x18): undefined reference to `main'
collect2: ld returned 1 exit status

Puzzled...

[Anders Blom]

Actually, these messages can be ignored. Apparently you have MPICC installed on your system, and this signals the GPAW setup.py script to attempt to compile GPAW in parallel for your machine. This fails (we don't really expect it to work anyway, as we haven't set it up), but the serial version is still installed first.

So, all should be fine, which you can verify by running the attached small test script, e.g. by dropping it on the Job Manager in VNL, or running "atkpython test_gpaw.py" on the command line.