Compilation of SIESTA-PEXSI

Asked by Pierre Capiod on 2019-03-14

Hi,

I have been trying to compile Siesta with the PEXSI library but at the very last compilation for the executable siesta file, here are the errors reported :

/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(lapack.o): In function `PEXSI::lapack::Potrf(char, int, float const*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/lapack.cpp:283: undefined reference to `spotrf_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(lapack.o): In function `PEXSI::lapack::Potrf(char, int, std::complex<float> const*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/lapack.cpp:335: undefined reference to `cpotrf_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(lapack.o): In function `PEXSI::lapack::Getrf(int, int, float*, int, int*)':
/nethome/capio001/local/pexsi_v0.9.2/src/lapack.cpp:391: undefined reference to `sgetrf_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(lapack.o): In function `PEXSI::lapack::Getrf(int, int, std::complex<float>*, int, int*)':
/nethome/capio001/local/pexsi_v0.9.2/src/lapack.cpp:443: undefined reference to `cgetrf_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(lapack.o): In function `PEXSI::lapack::Hegst(int, char, int, float*, int, float const*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/lapack.cpp:502: undefined reference to `ssygst_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(lapack.o): In function `PEXSI::lapack::Hegst(int, char, int, std::complex<float>*, int, std::complex<float> const*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/lapack.cpp:548: undefined reference to `chegst_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(lapack.o): In function `PEXSI::lapack::Trtri(char, char, int, float const*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/lapack.cpp:677: undefined reference to `strtri_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(lapack.o): In function `PEXSI::lapack::Trtri(char, char, int, std::complex<float> const*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/lapack.cpp:730: undefined reference to `ctrtri_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(lapack.o): In function `PEXSI::lapack::Lange(char, int, int, float*, int, float*)':
/nethome/capio001/local/pexsi_v0.9.2/src/lapack.cpp:1902: undefined reference to `slange_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(lapack.o): In function `PEXSI::lapack::Lange(char, int, int, std::complex<float>*, int, std::complex<float>*)':
/nethome/capio001/local/pexsi_v0.9.2/src/lapack.cpp:1910: undefined reference to `clange_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(lapack.o): In function `PEXSI::lapack::Lange(char, int, int, std::complex<double>*, int, std::complex<double>*)':
/nethome/capio001/local/pexsi_v0.9.2/src/lapack.cpp:1914: undefined reference to `zlange_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(lapack.o): In function `PEXSI::lapack::SingularValues(int, int, double*, int, double*)':
/nethome/capio001/local/pexsi_v0.9.2/src/lapack.cpp:1449: undefined reference to `dgesvd_'
/nethome/capio001/local/pexsi_v0.9.2/src/lapack.cpp:1455: undefined reference to `dgesvd_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(lapack.o): In function `PEXSI::lapack::QRSVD(int, int, double*, int, double*, double*, int, double*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/lapack.cpp:1249: undefined reference to `dgesvd_'
/nethome/capio001/local/pexsi_v0.9.2/src/lapack.cpp:1255: undefined reference to `dgesvd_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(lapack.o): In function `PEXSI::lapack::BidiagQRAlg(char, int, int, int, double*, double*, std::complex<double>*, int, std::complex<double>*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/lapack.cpp:937: undefined reference to `zbdsqr_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(lapack.o): In function `PEXSI::lapack::DivideAndConquerSVD(int, int, double*, int, double*, double*, int, double*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/lapack.cpp:1039: undefined reference to `dgesdd_'
/nethome/capio001/local/pexsi_v0.9.2/src/lapack.cpp:1045: undefined reference to `dgesdd_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(lapack.o): In function `PEXSI::lapack::SVDLeastSquare(int, int, int, float*, int, float*, int, float*, float, int*)':
/nethome/capio001/local/pexsi_v0.9.2/src/lapack.cpp:1599: undefined reference to `sgelss_'
/nethome/capio001/local/pexsi_v0.9.2/src/lapack.cpp:1606: undefined reference to `sgelss_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(lapack.o): In function `PEXSI::lapack::SingularValues(int, int, float*, int, float*)':
/nethome/capio001/local/pexsi_v0.9.2/src/lapack.cpp:1402: undefined reference to `sgesvd_'
/nethome/capio001/local/pexsi_v0.9.2/src/lapack.cpp:1408: undefined reference to `sgesvd_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(lapack.o): In function `PEXSI::lapack::QRSVD(int, int, float*, int, float*, float*, int, float*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/lapack.cpp:1200: undefined reference to `sgesvd_'
/nethome/capio001/local/pexsi_v0.9.2/src/lapack.cpp:1206: undefined reference to `sgesvd_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(lapack.o): In function `PEXSI::lapack::DivideAndConquerSVD(int, int, float*, int, float*, float*, int, float*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/lapack.cpp:988: undefined reference to `sgesdd_'
/nethome/capio001/local/pexsi_v0.9.2/src/lapack.cpp:994: undefined reference to `sgesdd_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(lapack.o): In function `PEXSI::lapack::BidiagQRAlg(char, int, int, int, float*, float*, std::complex<float>*, int, std::complex<float>*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/lapack.cpp:892: undefined reference to `cbdsqr_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(lapack.o): In function `PEXSI::lapack::BidiagQRAlg(char, int, int, int, float*, float*, float*, int, float*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/lapack.cpp:802: undefined reference to `sbdsqr_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(lapack.o): In function `PEXSI::lapack::SVDLeastSquare(int, int, int, std::complex<float>*, int, std::complex<float>*, int, float*, float, int*)':
/nethome/capio001/local/pexsi_v0.9.2/src/lapack.cpp:1701: undefined reference to `cgelss_'
/nethome/capio001/local/pexsi_v0.9.2/src/lapack.cpp:1708: undefined reference to `cgelss_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(lapack.o): In function `PEXSI::lapack::SingularValues(int, int, std::complex<float>*, int, float*)':
/nethome/capio001/local/pexsi_v0.9.2/src/lapack.cpp:1498: undefined reference to `cgesvd_'
/nethome/capio001/local/pexsi_v0.9.2/src/lapack.cpp:1504: undefined reference to `cgesvd_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(lapack.o): In function `PEXSI::lapack::QRSVD(int, int, std::complex<float>*, int, float*, std::complex<float>*, int, std::complex<float>*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/lapack.cpp:1300: undefined reference to `cgesvd_'
/nethome/capio001/local/pexsi_v0.9.2/src/lapack.cpp:1306: undefined reference to `cgesvd_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(lapack.o): In function `PEXSI::lapack::DivideAndConquerSVD(int, int, std::complex<float>*, int, float*, std::complex<float>*, int, std::complex<float>*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/lapack.cpp:1093: undefined reference to `cgesdd_'
/nethome/capio001/local/pexsi_v0.9.2/src/lapack.cpp:1099: undefined reference to `cgesdd_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(lapack.o): In function `PEXSI::lapack::SVDLeastSquare(int, int, int, std::complex<double>*, int, std::complex<double>*, int, double*, double, int*)':
/nethome/capio001/local/pexsi_v0.9.2/src/lapack.cpp:1753: undefined reference to `zgelss_'
/nethome/capio001/local/pexsi_v0.9.2/src/lapack.cpp:1760: undefined reference to `zgelss_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(lapack.o): In function `PEXSI::lapack::SingularValues(int, int, std::complex<double>*, int, double*)':
/nethome/capio001/local/pexsi_v0.9.2/src/lapack.cpp:1547: undefined reference to `zgesvd_'
/nethome/capio001/local/pexsi_v0.9.2/src/lapack.cpp:1553: undefined reference to `zgesvd_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(lapack.o): In function `PEXSI::lapack::QRSVD(int, int, std::complex<double>*, int, double*, std::complex<double>*, int, std::complex<double>*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/lapack.cpp:1351: undefined reference to `zgesvd_'
/nethome/capio001/local/pexsi_v0.9.2/src/lapack.cpp:1357: undefined reference to `zgesvd_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(lapack.o): In function `PEXSI::lapack::DivideAndConquerSVD(int, int, std::complex<double>*, int, double*, std::complex<double>*, int, std::complex<double>*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/lapack.cpp:1147: undefined reference to `zgesdd_'
/nethome/capio001/local/pexsi_v0.9.2/src/lapack.cpp:1153: undefined reference to `zgesdd_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(lapack.o): In function `PEXSI::lapack::Sygvd(int, char, char, int, double*, int, double*, int, double*)':
/nethome/capio001/local/pexsi_v0.9.2/src/lapack.cpp:643: undefined reference to `dsygvd_'
/nethome/capio001/local/pexsi_v0.9.2/src/lapack.cpp:650: undefined reference to `dsygvd_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Axpy(int, float, float const*, int, float*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:522: undefined reference to `saxpy_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Axpy(int, std::complex<float>, std::complex<float> const*, int, std::complex<float>*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:530: undefined reference to `caxpy_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Copy(int, float const*, int, float*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:541: undefined reference to `scopy_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Copy(int, std::complex<float> const*, int, std::complex<float>*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:547: undefined reference to `ccopy_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Dot(int, float const*, int, float const*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:553: undefined reference to `sdot_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Dotc(int, float const*, int, float const*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:575: undefined reference to `sdot_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Dotu(int, float const*, int, float const*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:597: undefined reference to `sdot_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Nrm2(int, float const*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:619: undefined reference to `snrm2_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Nrm2(int, std::complex<float> const*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:625: undefined reference to `scnrm2_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Scal(int, float, float*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:631: undefined reference to `sscal_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Scal(int, std::complex<float>, std::complex<float>*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:637: undefined reference to `cscal_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Gemv(char, int, int, float, float const*, int, float const*, int, float, float*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:652: undefined reference to `sgemv_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Gemv(char, int, int, std::complex<float>, std::complex<float> const*, int, std::complex<float> const*, int, std::complex<float>, std::complex<float>*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:669: undefined reference to `cgemv_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Ger(int, int, float, float const*, int, float const*, int, float*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:681: undefined reference to `sger_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Ger(int, int, std::complex<float>, std::complex<float> const*, int, std::complex<float> const*, int, std::complex<float>*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:693: undefined reference to `cgerc_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Gerc(int, int, float, float const*, int, float const*, int, float*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:705: undefined reference to `sger_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Gerc(int, int, std::complex<float>, std::complex<float> const*, int, std::complex<float> const*, int, std::complex<float>*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:717: undefined reference to `cgerc_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Geru(int, int, float, float const*, int, float const*, int, float*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:729: undefined reference to `sger_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Geru(int, int, std::complex<float>, std::complex<float> const*, int, std::complex<float> const*, int, std::complex<float>*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:741: undefined reference to `cgeru_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Hemv(char, int, float, float const*, int, float const*, int, float, float*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:753: undefined reference to `ssymv_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Hemv(char, int, std::complex<float>, std::complex<float> const*, int, std::complex<float> const*, int, std::complex<float>, std::complex<float>*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:765: undefined reference to `chemv_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Her(char, int, float, float const*, int, float*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:776: undefined reference to `ssyr_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Her(char, int, std::complex<float>, std::complex<float> const*, int, std::complex<float>*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:786: undefined reference to `cher_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Her2(char, int, float, float const*, int, float const*, int, float*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:797: undefined reference to `ssyr2_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Her2(char, int, std::complex<float>, std::complex<float> const*, int, std::complex<float> const*, int, std::complex<float>*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:809: undefined reference to `cher2_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Symv(char, int, float, float const*, int, float const*, int, float, float*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:821: undefined reference to `ssymv_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Symv(char, int, std::complex<float>, std::complex<float> const*, int, std::complex<float> const*, int, std::complex<float>, std::complex<float>*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:835: undefined reference to `csymv_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Syr(char, int, float, float const*, int, float*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:850: undefined reference to `ssyr_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Syr(char, int, std::complex<float>, std::complex<float> const*, int, std::complex<float>*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:862: undefined reference to `csyr_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Syr2(char, int, float, float const*, int, float const*, int, float*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:877: undefined reference to `ssyr2_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Syr2(char, int, std::complex<float>, std::complex<float> const*, int, std::complex<float> const*, int, std::complex<float>*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:898: undefined reference to `csyr2k_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Trmv(char, char, char, int, float const*, int, float*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:920: undefined reference to `strmv_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Trmv(char, char, char, int, std::complex<float> const*, int, std::complex<float>*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:930: undefined reference to `ctrmv_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Trsv(char, char, char, int, float const*, int, float*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:940: undefined reference to `strsv_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Trsv(char, char, char, int, std::complex<float> const*, int, std::complex<float>*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:950: undefined reference to `ctrsv_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Gemm(char, char, int, int, int, float, float const*, int, float const*, int, float, float*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:968: undefined reference to `sgemm_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Gemm(char, char, int, int, int, std::complex<float>, std::complex<float> const*, int, std::complex<float> const*, int, std::complex<float>, std::complex<float>*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:989: undefined reference to `cgemm_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Hemm(char, char, int, int, float, float const*, int, float const*, int, float, float*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:1007: undefined reference to `ssymm_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Hemm(char, char, int, int, std::complex<float>, std::complex<float> const*, int, std::complex<float> const*, int, std::complex<float>, std::complex<float>*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:1025: undefined reference to `chemm_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Her2k(char, char, int, int, float, float const*, int, float const*, int, float, float*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:1044: undefined reference to `ssyr2k_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Her2k(char, char, int, int, std::complex<float>, std::complex<float> const*, int, std::complex<float> const*, int, std::complex<float>, std::complex<float>*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:1063: undefined reference to `cher2k_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Herk(char, char, int, int, float, float const*, int, float, float*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:1081: undefined reference to `ssyrk_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Herk(char, char, int, int, std::complex<float>, std::complex<float> const*, int, std::complex<float>, std::complex<float>*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:1097: undefined reference to `cherk_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Symm(char, char, int, int, float, float const*, int, float const*, int, float, float*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:1111: undefined reference to `ssymm_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Symm(char, char, int, int, std::complex<float>, std::complex<float> const*, int, std::complex<float> const*, int, std::complex<float>, std::complex<float>*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:1129: undefined reference to `csymm_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Syr2k(char, char, int, int, float, float const*, int, float const*, int, float, float*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:1147: undefined reference to `ssyr2k_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Syr2k(char, char, int, int, std::complex<float>, std::complex<float> const*, int, std::complex<float> const*, int, std::complex<float>, std::complex<float>*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:1165: undefined reference to `csyr2k_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Syrk(char, char, int, int, float, float const*, int, float, float*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:1181: undefined reference to `ssyrk_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Syrk(char, char, int, int, std::complex<float>, std::complex<float> const*, int, std::complex<float>, std::complex<float>*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:1193: undefined reference to `csyrk_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Trmm(char, char, char, char, int, int, float, float const*, int, float*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:1207: undefined reference to `strmm_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Trmm(char, char, char, char, int, int, std::complex<float>, std::complex<float> const*, int, std::complex<float>*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:1224: undefined reference to `ctrmm_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Trsm(char, char, char, char, int, int, float, float const*, int, float*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:1241: undefined reference to `strsm_'
/scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a(blas.o): In function `PEXSI::blas::Trsm(char, char, char, char, int, int, std::complex<float>, std::complex<float> const*, int, std::complex<float>*, int)':
/nethome/capio001/local/pexsi_v0.9.2/src/blas.cpp:1258: undefined reference to `ctrsm_'

It seems either a not good version of Lapack/Blas (which I find it odd since I have tried with 2 different versions of Lapack and Blas in that case) or it cannot find the library ?
I have been trying to play with the -DAdd_ flag in the pexsi compilation but the error is the same.
Here is my make file.

#
# Copyright (C) 1996-2016 The SIESTA group
# This file is distributed under the terms of the
# GNU General Public License: see COPYING in the top directory
# or http://www.gnu.org/copyleft/gpl.txt.
# See Docs/Contributors.txt for a list of contributors.
#
.SUFFIXES:
.SUFFIXES: .f .F .o .a .f90 .F90 .c

SIESTA_ARCH=x86_64-unknown-linux-gnu--unknown

FPP=
FPP_OUTPUT=
FC=mpif90
RANLIB=ranlib

SYS=nag

SP_KIND=4
DP_KIND=8
KINDS=$(SP_KIND) $(DP_KIND)

FFLAGS=-g -O2
FPPFLAGS= -DMPI -DFC_HAVE_FLUSH -DFC_HAVE_ABORT -DSIESTA__PEXSI
LDFLAGS=
INCFLAGS=-I/nethome/capio001/local/pexsi_v0.9.2/build/include

ARFLAGS_EXTRA=

FCFLAGS_fixed_f=
FCFLAGS_free_f90=
FPPFLAGS_fixed_F=
FPPFLAGS_free_F90=

BLAS_LIBS=/scratch2/nethome/capio001/local/blas/libblas.a
LAPACK_LIBS=/scratch2/nethome/capio001/local/lapack/lapack-3.8.0/liblapack.a
BLACS_LIBS=-lblacsF77init -lblacs -lblacsF77init
SCALAPACK_LIBS=/cm/shared/apps/scalapack/gcc/1.8.0/lib64/libscalapack.a
PEXSI_LIBS= /scratch2/nethome/capio001/local/pexsi_v0.9.2/build/lib/libpexsi_linux_v0.9.2.a
PARMETIS_LIBS=/scratch2/nethome/capio001/local/parmetis-4.0.3/build/Linux-x86_64/libparmetis/libparmetis.a
METIS_LIBS=/scratch2/nethome/capio001/local/parmetis-4.0.3/build/Linux-x86_64/libmetis/libmetis.a
SUPERLU_LIBS=/scratch2/nethome/capio001/local/SuperLU_DIST_4.3/lib/libsuperlu_dist_4.3.a

NETCDF_LIBS=
NETCDF_INTERFACE=

LIBS=$(SCALAPACK_LIBS) $(BLACS_LIBS) $(LAPACK_LIBS) $(BLAS_LIBS) $(NETCDF_LIBS) $(PEXSI_LIBS) $(PARMETIS_LIBS) $(METIS_LIBS) $(SUPERLU_LIBS)
LIBS += -lstdc++ -lmpi_cxx -Wl,--allow-multiple-definition

#SIESTA needs an F90 interface to MPI
#This will give you SIESTA's own implementation
#If your compiler vendor offers an alternative, you may change
#to it here.
MPI_INTERFACE=libmpi_f90.a
MPI_INCLUDE=.

#Dependency rules are created by autoconf according to whether
#discrete preprocessing is necessary or not.
.F.o:
 $(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_fixed_F) $<
.F90.o:
 $(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_free_F90) $<
.f.o:
 $(FC) -c $(FFLAGS) $(INCFLAGS) $(FCFLAGS_fixed_f) $<
.f90.o:
 $(FC) -c $(FFLAGS) $(INCFLAGS) $(FCFLAGS_free_f90) $<

If you need any additional information, please let me know

Pierre

Question information

Language:
English Edit question
Status:
Solved
For:
Siesta Edit question
Assignee:
No assignee Edit question
Solved by:
Nick Papior
Solved:
2019-03-14
Last query:
2019-03-14
Last reply:
2019-03-14
Best Nick Papior (nickpapior) said : #1

You should move your SCALAPACK libraries and LAPACK libraries to the *end* of your LIBS variable.

Pierre Capiod (pierre.capiod) said : #2

Hi Nick,

Thanks, it did the trick.
Though, I might open a new thread for a question, but PEXSI doesn't like the Auxiliary supercell, even with a large slab (600 atoms), Siesta wants to use an internal aux supercell, even with the "ForceAuxCell" set to false.

Here is my .fdf

SystemName cu111_test_pexsi
SystemLabel cu111_test_pexsi

NumberOfSpecies 1
NumberOfAtoms 600
%block ChemicalSpecieslabel
    1 29 Cu.gga.4sp_2.1
%endblock ChemicalSpecieslabel

%block PAO.Basis
Cu.gga.4sp_2.1 3
n=3 2 3 P 1
8.9 2.2 3.7

n=4 0 3 P 1
8.3 3.7 5.6

n=4 1 3 P 1
9.0 5.7 5.6

%endblock PAO.Basis

LatticeConstant 1.0 Ang
%block LatticeVectors
    25.526554800834369 0.000000000000000 0.000000000000000
    12.763277400417184 22.106644928618181 0.000000000000000
    0.000000000000000 0.000000000000000 22.421172358872745
%endblock LatticeVectors

AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
     1.276327740 0.736888164 6.000000000 1
     3.828983220 0.736888164 6.000000000 1
     6.381638700 0.736888164 6.000000000 1
     8.934294180 0.736888164 6.000000000 1
    11.486949660 0.736888164 6.000000000 1
    14.039605140 0.736888164 6.000000000 1
    16.592260621 0.736888164 6.000000000 1
    19.144916101 0.736888164 6.000000000 1
    21.697571581 0.736888164 6.000000000 1
    24.250227061 0.736888164 6.000000000 1
     2.552655480 2.947552657 6.000000000 1
     5.105310960 2.947552657 6.000000000 1
     7.657966440 2.947552657 6.000000000 1
    10.210621920 2.947552657 6.000000000 1
    12.763277400 2.947552657 6.000000000 1
    15.315932881 2.947552657 6.000000000 1
    17.868588361 2.947552657 6.000000000 1
    20.421243841 2.947552657 6.000000000 1
    22.973899321 2.947552657 6.000000000 1
    25.526554801 2.947552657 6.000000000 1
     3.828983220 5.158217150 6.000000000 1
     6.381638700 5.158217150 6.000000000 1
     8.934294180 5.158217150 6.000000000 1
    11.486949660 5.158217150 6.000000000 1
    14.039605140 5.158217150 6.000000000 1
    16.592260621 5.158217150 6.000000000 1
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     5.105310960 7.368881643 6.000000000 1
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     8.934294180 14.000875121 6.000000000 1
    11.486949660 14.000875121 6.000000000 1
    14.039605140 14.000875121 6.000000000 1
    16.592260621 14.000875121 6.000000000 1
    19.144916101 14.000875121 6.000000000 1
    21.697571581 14.000875121 6.000000000 1
    24.250227061 14.000875121 6.000000000 1
    26.802882541 14.000875121 6.000000000 1
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    12.763277400 16.211539614 6.000000000 1
    15.315932881 16.211539614 6.000000000 1
    17.868588361 16.211539614 6.000000000 1
    20.421243841 16.211539614 6.000000000 1
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     0.000000000 1.473776329 8.084234472 1
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     7.657966440 1.473776329 8.084234472 1
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     5.105310960 5.895105314 8.084234472 1
     7.657966440 5.895105314 8.084234472 1
    10.210621920 5.895105314 8.084234472 1
    12.763277400 5.895105314 8.084234472 1
    15.315932881 5.895105314 8.084234472 1
    17.868588361 5.895105314 8.084234472 1
    20.421243841 5.895105314 8.084234472 1
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     3.828983220 8.105769807 8.084234472 1
     6.381638700 8.105769807 8.084234472 1
     8.934294180 8.105769807 8.084234472 1
    11.486949660 8.105769807 8.084234472 1
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%endblock AtomicCoordinatesAndAtomicSpecies

PAO.EnergyShift 0.09999997 eV
%block PS.lmax
Cu.gga.4sp_2.1 2
%endblock PS.lmax
XC.functional GGA
XC.authors PBE
MaxSCFIterations 600
DM.MixingWeight 0.05
DM.NumberPulay 8
DM.UseSaveDM true
DM.Tolerance 5e-6 eV
DM.Require.Energy.Convergence true
MeshCutoff 4081.7079 eV
ForceAuxCell false
SolutionMethod PEXSI
WriteEigenvalues false
ElectronicTemperature 0.00035000 eV
%block BandLines
1 0.5 0.0 0.0 M
200 0.333333 0.333333 0.0 K
200 0.0 0.0 0.0 G
200 0.5 0.0 0.0 M
%endblock BandLines
WriteKbands false
WriteBands false
WFS.Write.For.Bands false
WriteWaveFunctions false
%block LocalDensityOfStates
-5.200 -4.20 eV
%endblock LocalDensityOfStates
COOP.Write false
WFS.Energy.Min -10 eV
WFS.Energy.Max 10 eV
SlabDipoleCorrection true
SaveRho true
SaveElectrostaticPotential true
SaveTotalPotential true
SaveTotalCharge true
SaveBaderCharge true
WriteDenchar true
MD.TypeOfRun CG
MD.MaxForceTol 0.04000000 eV/Ang
WriteMDhistory true
%block GeometryConstraints
atom from 1 to 2
%endblock GeometryConstraints

#KPoint grid
%block kgrid_Monkhorst_Pack
     12 0 0 0.0
     0 12 0 0.0
     0 0 1 0.0
%endblock kgrid_Monkhorst_Pack

Thanks for your help !

Pierre Capiod (pierre.capiod) said : #3

Thanks Nick Papior, that solved my question.