You compiler (gnu 4.8.5) is *very* old. Please upgrade to a modern version.
Best regards, Alberto ----- El 6 de Junio de 2024, a las 19:09, Boubacar Traore <[email protected]> escribió: | I finally sorted out the issue of scalapack linking by adding its path to | LIBRARY_PATH instead of LD_LIBRARY_PATH (more info here: [ | https://urldefense.com/v3/__https://stackoverflow.com/questions/47105835/ld-library-path-is-ignored-by-gcc__;!!D9dNQwwGXtA!UKXFsN93oU7fdjctS5itiA2CMH4YTUW-VUxSJl8f5ejE_wN2ffrRXxBautffKqwBfEnjMj-Kg2AAYGfMdi0$ | | | https://urldefense.com/v3/__https://stackoverflow.com/questions/47105835/ld-library-path-is-ignored-by-gcc__;!!D9dNQwwGXtA!WikrDz3RbFwqReRTUxLQfCcPc8VFr9BlO-JUJkIQug1Z9u1DQHc_ER-m8pNnzqj6DLgZxZVP-L5VhTVb$ | ] ). | I used this for cmake build stage: | $ cmake -S. -B_build -DCMAKE_INSTALL_PREFIX=/home/boubacart/SIESTA/siesta/bin | -DSIESTA_WITH_MPI=ON -DSIESTA_WITH_ELPA=ON | -DSCALAPACK_LIBRARY_DIR=/usr/lib64/openmpi/lib | -DSCALAPACK_LIBRARY="-lscalapack" | The config steps then succeeds. | However, I encounter other issues during the compilation stage and I am not sure | what is the problem and from the start it issues errors regarding some | deferred-length character : | =============== | [ 0%] Building Fortran object | _deps/libfdf-build/CMakeFiles/libfdf-lib.dir/src/prec.F90.o | [ 0%] Building Fortran object | _deps/mctc-lib-build/CMakeFiles/mctc-lib-lib.dir/src/mctc/env/accuracy.f90.o | [ 0%] Building Fortran object | _deps/xmlf90-build/CMakeFiles/xmlf90-lib.dir/src/wxml/m_wxml_array_str.f90.o | [ 0%] Building Fortran object | _deps/libfdf-build/CMakeFiles/libfdf-lib.dir/src/utils.F90.o | [ 0%] Building Fortran object | _deps/libgridxc-build/CMakeFiles/libgridxc-lib.dir/src/alloc.F90.o | [ 0%] Building Fortran object | _deps/mctc-lib-build/CMakeFiles/mctc-lib-lib.dir/src/mctc/env/error.f90.o | /home/boubacart/SIESTA/siesta-5.0.0/_build/_deps/mctc-lib-src/src/mctc/env/error.f90:46.46: | character(len=:), allocatable :: message | 1 | Error: Deferred-length character component 'message' at (1) is not yet supported | /home/boubacart/SIESTA/siesta-5.0.0/_build/_deps/mctc-lib-src/src/mctc/env/error.f90:46.46: | character(len=:), allocatable :: message | 1 | Error: Deferred-length character component 'message' at (1) is not yet supported | gmake[2]: *** | [_deps/mctc-lib-build/CMakeFiles/mctc-lib-lib.dir/src/mctc/env/error.f90.o] | Error 1 | gmake[1]: *** [_deps/mctc-lib-build/CMakeFiles/mctc-lib-lib.dir/all] Error 2 | gmake[1]: *** Waiting for unfinished jobs.... | [ 0%] Building Fortran object | _deps/libgridxc-build/CMakeFiles/libgridxc-lib.dir/src/precision.F90.o | [ 0%] Building Fortran object | _deps/xmlf90-build/CMakeFiles/xmlf90-lib.dir/src/wxml/m_wxml_error.f90.o | [ 0%] Building Fortran object | _deps/libgridxc-build/CMakeFiles/libgridxc-lib.dir/src/sys.F90.o | [ 0%] Building Fortran object | _deps/xmlf90-build/CMakeFiles/xmlf90-lib.dir/src/wxml/m_wxml_escape.f90.o | .. | .. | .. | [ 2%] Building Fortran object | _deps/xmlf90-build/CMakeFiles/xmlf90-lib.dir/src/dom/m_dom_parse.f90.o | [ 2%] Building Fortran object | _deps/libgridxc-build/CMakeFiles/libgridxc-lib.dir/src/debugxc.F90.o | [ 3%] Building Fortran object | _deps/xmlf90-build/CMakeFiles/xmlf90-lib.dir/src/xpath/xmlf90_xpath.f90.o | [ 3%] Building Fortran object | _deps/libgridxc-build/CMakeFiles/libgridxc-lib.dir/src/vv_vdwxc.F90.o | [ 3%] Building Fortran object | _deps/xmlf90-build/CMakeFiles/xmlf90-lib.dir/src/dom/xmlf90_dom.f90.o | [ 3%] Linking Fortran static library libxmlf90.a | [ 3%] Built target xmlf90-lib | [ 3%] Building Fortran object | _deps/libgridxc-build/CMakeFiles/libgridxc-lib.dir/src/fft3d.F90.o | /home/boubacart/SIESTA/siesta-5.0.0/_build/_deps/libgridxc-src/src/fft3d.F90:234.25: | call c_f_pointer(c_loc(aDat(:,:,:,1)),aux1,[aMesh(1)*aMesh(2)*aMesh(3)]) | 1 | Warning: Array section in 'c_loc' call at (1) | /home/boubacart/SIESTA/siesta-5.0.0/_build/_deps/libgridxc-src/src/fft3d.F90:235.25: | call c_f_pointer(c_loc(aDat(:,:,:,2)),aux2,[aMesh(1)*aMesh(2)*aMesh(3)]) | 1 | Warning: Array section in 'c_loc' call at (1) | /home/boubacart/SIESTA/siesta-5.0.0/_build/_deps/libgridxc-src/src/fft3d.F90:249.28: | call c_f_pointer(c_loc(aDat(:,:,i3,1)),aux1,[aMesh(1)*aMesh(2)]) | 1 | Warning: Array section in 'c_loc' call at (1) | /home/boubacart/SIESTA/siesta-5.0.0/_build/_deps/libgridxc-src/src/fft3d.F90:250.28: | call c_f_pointer(c_loc(aDat(:,:,i3,2)),aux2,[aMesh(1)*aMesh(2)]) | 1 | Warning: Array section in 'c_loc' call at (1) | /home/boubacart/SIESTA/siesta-5.0.0/_build/_deps/libgridxc-src/src/fft3d.F90:263.25: | call c_f_pointer(c_loc(aDat(:,:,:,1)),aux1,[aMesh(1)*aMesh(2)*aMesh(3)]) | 1 | Warning: Array section in 'c_loc' call at (1) | /home/boubacart/SIESTA/siesta-5.0.0/_build/_deps/libgridxc-src/src/fft3d.F90:264.25: | call c_f_pointer(c_loc(aDat(:,:,:,2)),aux2,[aMesh(1)*aMesh(2)*aMesh(3)]) | 1 | Warning: Array section in 'c_loc' call at (1) | [ 3%] Building Fortran object | _deps/libgridxc-build/CMakeFiles/libgridxc-lib.dir/src/vdwxc.F90.o | [ 4%] Building Fortran object | _deps/libgridxc-build/CMakeFiles/libgridxc-lib.dir/src/fftr.F90.o | [ 4%] Building Fortran object | _deps/libgridxc-build/CMakeFiles/libgridxc-lib.dir/src/xcmod.F90.o | [ 4%] Building Fortran object | _deps/libgridxc-build/CMakeFiles/libgridxc-lib.dir/src/cellxc.F90.o | [ 4%] Building Fortran object | _deps/libgridxc-build/CMakeFiles/libgridxc-lib.dir/src/atomxc.F90.o | [ 4%] Building Fortran object | _deps/libgridxc-build/CMakeFiles/libgridxc-lib.dir/src/gridxc.F90.o | [ 4%] Linking Fortran static library libgridxc.a | [ 4%] Built target libgridxc-lib | gmake: *** [all] Error 2 | Time spent in user mode (CPU seconds) : 16.861s | Time spent in kernel mode (CPU seconds) : 1.792s | Total time : 0:07.27s | CPU utilisation (percentage) : 256.5% | Times the process was swapped : 0 | Times of major page faults : 1 | Times of minor page faults : 863847 | =========================================== | Anyone have an idea about solutions to this ? | Thanks, | Boubacar | On Thu, 6 Jun 2024 at 09:25, Boubacar Traore < [ mailto:[email protected] | | [email protected] ] > wrote: || More specifically it stops at scalapack stage when : || "-- Performing Test scalapack_has_blacs_gridinit - Failed" || The config routine finds scalapack but it fails in "SiestaCheckLinalg.cmake" || routine. || All the dependencies were installed according to the doc. So, I am not sure if I || still missed something or if it is a bug ? || Thanks, || Boubacar || On Wed, 5 Jun 2024 at 21:54, Boubacar Traore < [ mailto:[email protected] | || [email protected] ] > wrote: ||| Hi, ||| I am trying to compile siesta with cmake but I encounter issues with scalapack ||| linking. I notice that the compilation process has changed compared to what I ||| was used to. ||| Here is my cmake build command: ||| $ cmake -S. -B_build -DCMAKE_INSTALL_PREFIX=/home/boubacart/SIESTA/siesta/bin ||| -DSIESTA_WITH_MPI=ON -DSIESTA_WITH_ELPA=ON -DSIESTA_WITH_LIBXC=ON ||| -DSCALAPACK_LIBRARY="-lscalapack-openmpi-devel" ||| It fails at with a linking error as shown below: ||| =================================== ||| -- The Fortran compiler identification is GNU 4.8.5 ||| -- The C compiler identification is GNU 4.8.5 ||| -- Detecting Fortran compiler ABI info ||| -- Detecting Fortran compiler ABI info - done ||| -- Check for working Fortran compiler: /bin/f95 - skipped ||| -- Detecting C compiler ABI info ||| -- Detecting C compiler ABI info - done ||| -- Check for working C compiler: /bin/cc - skipped ||| -- Detecting C compile features ||| -- Detecting C compile features - done ||| -- Check use of deprecated variables ||| -- All Siesta variables/options are prefixed with SIESTA_, e.g. SIESTA_WITH_MPI ||| -- Check use of deprecated variables - success ||| -- Using GNU compiler ||| -- Using toolchain: Config/cmake/toolchains/gnu.cmake ||| -- ||| No build type selected. SIESTA will default to 'Release'. ||| To override pass -DCMAKE_BUILD_TYPE=<type> in order to configure SIESTA. ||| Available options are: ||| * -DCMAKE_BUILD_TYPE=Release - For an optimized build with no assertions or ||| debug info. ||| * -DCMAKE_BUILD_TYPE=Debug - For an unoptimized build with assertions and debug ||| info. ||| * -DCMAKE_BUILD_TYPE=Check - For an unoptimized build with assertions and debug ||| info + code checks. ||| * -DCMAKE_BUILD_TYPE=RelWithDebInfo - For an optimized build with no assertions ||| but with debug info. ||| * -DCMAKE_BUILD_TYPE=MinSizeRel - For a build optimized for size instead of ||| speed. ||| -- Flags for C-compiler (build type: Release): -O3 -march=native ||| -- Flags for Fortran-compiler (build type: Release): -O3 -march=native ||| -- Found PkgConfig: /bin/pkg-config (found version "0.27.1") ||| -- Checking Siesta version ||| -- SIESTA_VERSION: 5.1-MaX-28-gf3224d62e (err=3) ||| -- ||| WARNING: This is *not* an official SIESTA release. ||| WARNING: ||| WARNING: Unless you are trying a feature or fix that has not ||| WARNING: been released yet, we strongly recommend the use of ||| WARNING: official releases of SIESTA, which can be downloaded from ||| WARNING: [ ||| https://urldefense.com/v3/__https://gitlab.com/siesta-project/siesta/-/releases__;!!D9dNQwwGXtA!UKXFsN93oU7fdjctS5itiA2CMH4YTUW-VUxSJl8f5ejE_wN2ffrRXxBautffKqwBfEnjMj-Kg2AAMxgnUgg$ ||| | https://urldefense.com/v3/__https://gitlab.com/siesta-project/siesta/-/releases__;!!D9dNQwwGXtA!WikrDz3RbFwqReRTUxLQfCcPc8VFr9BlO-JUJkIQug1Z9u1DQHc_ER-m8pNnzqj6DLgZxZVP-AFm6iAm$ ] ||| -- Checking Siesta version - found development version ||| -- Parsing BLAS options ||| -- Locating BLAS library ||| -- Looking for Fortran sgemm ||| -- Looking for Fortran sgemm - not found ||| -- Performing Test CMAKE_HAVE_LIBC_PTHREAD ||| -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed ||| -- Looking for pthread_create in pthreads ||| -- Looking for pthread_create in pthreads - not found ||| -- Looking for pthread_create in pthread ||| -- Looking for pthread_create in pthread - found ||| -- Found Threads: TRUE ||| -- Looking for Fortran sgemm ||| -- Looking for Fortran sgemm - found ||| -- Found BLAS: /usr/lib64/libblas.so ||| -- Found CustomBlas: /usr/lib64/libblas.so ||| -- Locating BLAS library - found ||| -- BLAS library: /usr/lib64/libblas.so ||| -- BLAS link flags: ||| -- Parsing LAPACK options ||| -- Locating LAPACK library ||| -- Looking for Fortran cheev ||| -- Looking for Fortran cheev - not found ||| -- Looking for Fortran cheev ||| -- Looking for Fortran cheev - found ||| -- Found LAPACK: /usr/lib64/liblapack.so;/usr/lib64/libblas.so ||| -- Found CustomLapack: /usr/lib64/liblapack.so;/usr/lib64/libblas.so ||| -- Locating LAPACK library - found ||| -- LAPACK library: /usr/lib64/liblapack.so;/usr/lib64/libblas.so ||| -- LAPACK link flags: ||| -- Found MPI_C: /usr/lib64/openmpi/lib/libmpi.so (found version "3.0") ||| -- Found MPI_Fortran: /usr/lib64/openmpi/lib/libmpi_usempi.so (found version ||| "3.0") ||| -- Found MPI: TRUE (found version "3.0") found components: Fortran C ||| -- Parsing ScaLAPACK options ||| -- Locating ScaLAPACK library ||| -- Using user-defined variables ||| -- Found CustomScalapack: -lscalapack-openmpi-devel ||| -- Locating ScaLAPACK library - found ||| -- ScaLAPACK library: -lscalapack-openmpi-devel ||| -- ScaLAPACK link flags: ||| -- Checking that BLAS library works... ||| -- Performing Test blas_has_sgemm ||| -- Performing Test blas_has_sgemm - Success ||| -- Performing Test blas_cdotu_return_convention ||| -- Performing Test blas_cdotu_return_convention - Success ||| -- Checking that LAPACK library works... ||| -- Performing Test lapack_has_dsysv ||| -- Performing Test lapack_has_dsysv - Success ||| -- Checking that ScaLAPACK library works... ||| -- Performing Test scalapack_has_blacs_gridinit ||| -- Performing Test scalapack_has_blacs_gridinit - Failed ||| CMake Warning at Config/cmake/SiestaCheckLinalg.cmake:125 (message): ||| --------------------------------------------- ||| ScaLAPACK library cannot link properly Please check the library linking string ||| found or used by CMake--------------------------------------------- ||| Call Stack (most recent call first): ||| CMakeLists.txt:189 (include) ||| CMake Error at Config/cmake/SiestaCheckLinalg.cmake:130 (message): ||| *** ScaLAPACK library does not link properly ||| Call Stack (most recent call first): ||| CMakeLists.txt:189 (include) ||| -- Configuring incomplete, errors occurred! ||| =================================== ||| Can anyone help me solve this issue? I tried but I so far did not find a ||| solution. ||| Thanks, ||| Boubacar | -- | SIESTA is supported by the Spanish Research Agency (AEI) and by the European | H2020 MaX Centre of Excellence | (https://urldefense.com/v3/__http://www.max-centre.eu/__;!!D9dNQwwGXtA!Ur3mYMzmBYqYxB8SxtLvkDxXwBqLomhmZmzAYOZO1h3dx_Uxi6JP0997AuAsq7Y_eDKB5HWJjDkFyKgai97G$ | )
-- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
