Quick Questions about scuff-cas3D
Closed this issue · 8 comments
Hi Homer,
I am a beginner of using scuff-em to calculate Casimir Force. Yesterday I tested the command scuff-cas3D with the example SiliconBeams. However I found it was much more time consuming than I expected, and there are something I did not quite understand when I used 'tail' command to track the progress of calculation.
When I run the scuff-cas3D with at single frequency with command --Xi. It seems that every it complete one round calculation from transform 1.0 to transform 5.0, it will go back to transform 1.0 to calculate again. But it does not clearly show other information about the calculation. So I am confused why it will go back again and again to calculation many time for one frequency? And how long will it take to complete a calculation at specific frequency or a full fun?
Thank you,
Xingyu
And I also met another problem when I tried to install scuff-em on clusters which uses CentOS system. As this cluster is owned by the university, I do not have the privileges to use sudo to install package. So I installed all the required package like OpenBLAS by compiling from source. However when I run the 'sh autogen.sh' command, it always shows an error:
configure: error: BLAS not found!
I tried to fix the problem by adding the bin/lib path of OpenBLAS to .bashrc file, but this problem still existed.
I don't know I happens as I already installed the OpenBLAS package.
I tried to fix the problem by adding the bin/lib path of OpenBLAS to .bashrc file, but this problem still existed.
Could you be more specific on what exactly did you put there? You should check that you really have set the environment variables correctly (e.g. running env).
I tried to fix the problem by adding the bin/lib path of OpenBLAS to .bashrc file, but this problem still existed.
Could you be more specific on what exactly did you put there? You should check that you really have set the environment variables correctly (e.g. running
env).
I wrote:
export PATH=/home/gao477/OpenBLAS/bin:$PATH
export LD_LIBRARY_PATH=/home/gao477/OpenBLAS/lib:$LD_LIBRARY_PATH
to the ~/.bashrc file.
And after using 'source ~/.bashrc', the 'env' command shows that:
LD_LIBRARY_PATH=/home/gao477/scheme/lib:/home/gao477/ncurse/lib:/home/gao477/OpenBLAS/lib:/apps/cent7/intel/impi/2017.1.132/lib64:/apps/cent7/intel/itac/2017.1.024/intel64/slib:/apps/cent7/intel/itac/2017.1.024/lib:/apps/cent7/intel/compilers_and_libraries_2017.1.132/linux/compiler/lib/intel64:/apps/cent7/intel/compilers_and_libraries_2017.1.132/linux/ipp/lib/intel64:/apps/cent7/intel/compilers_and_libraries_2017.1.132/linux/mkl/lib/intel64:/apps/cent7/intel/compilers_and_libraries_2017.1.132/linux/tbb/lib/intel64/gcc4.7:/apps/cent7/intel/opencl-1.2-sdk-6.3.0.1904/lib64:/opt/thinlinc/lib64:/opt/thinlinc/lib
PATH=/home/gao477/scheme/bin:/home/gao477/ncurse/bin:/home/gao477/OpenBLAS/bin:/opt/moab/bin:/usr/lib64/qt-3.3/bin:/apps/cent7/xalt/bin:/apps/cent7/intel/impi/2017.1.132/bin64:/apps/cent7/intel/itac/2017.1.024/bin:/apps/cent7/intel/compilers_and_libraries_2017.1.132/linux/bin/intel64:/apps/cent7/intel/inspector_2017.1.1.484836/bin64:/apps/cent7/intel/advisor_2017.1.1.486553/bin64:/apps/cent7/intel/vtune_amplifier_xe_2017/bin64:/apps/cent7/intel/opencl-1.2-sdk-6.3.0.1904/bin:/opt/moab/bin:/bin:/usr/bin:/opt/thinlinc/bin:/usr/local/bin:/usr/bin/X11:/sbin:/usr/sbin:/usr/local/sbin:/opt/hpss/bin:/opt/hsi/bin:/opt/ibutils/bin:/opt/moab/bin:/opt/hpss/bin:/opt/hsi/bin:/opt/moab/bin
And I also used
sh autogen.sh --prefix=/home/gao477/packages/scuff-em -v LIBS=-ldl LDFLAGS="-L/home/gao477/OpenBLAS/lib -L/home/gao477/Downloads/hdf5-1.10.5/hdf5/lib -L/usr/local/lib" CPPFLAGS="-I/home/gao477/OpenBLAS/include -I/usr/local/include -I/home/gao477/Downloads/hdf5-1.10.5/hdf5/include"
when I run sh autogen.sh . With these options, hdf5 can be found, but OpenBLAS still cannot be found. But this afternoon I tried to install MPB package which also requires OpenBLAS. Without -L/home/gao477/OpenBLAS/lib and -I/home/gao477/OpenBLAS/include, MPB also showed an error of BLAS not found. After adding these two options, it was installed successfully.
autoreconf: Entering directory .' autoreconf: configure.ac: not using Gettext autoreconf: running: aclocal --force -I m4 autoreconf: configure.ac: tracing autoreconf: running: libtoolize --force libtoolize: putting auxiliary files in .'.
libtoolize: linking file ./ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIR, m4'.
libtoolize: linking file m4/libtool.m4' libtoolize: linking file m4/ltoptions.m4'
libtoolize: linking file m4/ltsugar.m4' libtoolize: linking file m4/ltversion.m4'
libtoolize: linking file m4/lt~obsolete.m4' autoreconf: running: /usr/bin/autoconf --force autoreconf: running: /usr/bin/autoheader --force autoreconf: running: automake --add-missing --force-missing autoreconf: Leaving directory .'
autoreconf: Entering directory .' autoreconf: configure.ac: not using Gettext autoreconf: running: aclocal --force -I m4 autoreconf: configure.ac: tracing autoreconf: running: libtoolize --force libtoolize: putting auxiliary files in .'.
libtoolize: linking file ./ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIR, m4'.
libtoolize: linking file m4/libtool.m4' libtoolize: linking file m4/ltoptions.m4'
libtoolize: linking file m4/ltsugar.m4' libtoolize: linking file m4/ltversion.m4'
libtoolize: linking file m4/lt~obsolete.m4' autoreconf: running: /usr/bin/autoconf --force autoreconf: running: /usr/bin/autoheader --force autoreconf: running: automake --add-missing --force-missing autoreconf: Leaving directory .'
autoreconf: Entering directory .' autoreconf: configure.ac: not using Gettext autoreconf: running: aclocal --force -I m4 autoreconf: configure.ac: tracing autoreconf: running: libtoolize --force libtoolize: putting auxiliary files in .'.
libtoolize: linking file ./ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIR, m4'.
libtoolize: linking file m4/libtool.m4' libtoolize: linking file m4/ltoptions.m4'
libtoolize: linking file m4/ltsugar.m4' libtoolize: linking file m4/ltversion.m4'
libtoolize: linking file m4/lt~obsolete.m4' autoreconf: running: /usr/bin/autoconf --force autoreconf: running: /usr/bin/autoheader --force autoreconf: running: automake --add-missing --force-missing autoreconf: Leaving directory .'
checking for a BSD-compatible install... /bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking how to print strings... printf
checking for style of include used by make... GNU
checking for gcc... mpiicc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether mpiicc accepts -g... yes
checking for mpiicc option to accept ISO C89... none needed
checking dependency style of mpiicc... gcc3
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for ld used by mpiicc... /apps/cent7/xalt/bin/ld
checking if the linker (/apps/cent7/xalt/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /bin/nm -B
checking the name lister (/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 3458764513820540925
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /apps/cent7/xalt/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @file support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /bin/nm -B output from mpiicc object... ok
checking for sysroot... no
checking for mt... no
checking if : is a manifest tool... no
checking how to run the C preprocessor... mpiicc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if mpiicc supports -fno-rtti -fno-exceptions... yes
checking for mpiicc option to produce PIC... -fPIC -DPIC
checking if mpiicc PIC flag -fPIC -DPIC works... yes
checking if mpiicc static flag -static works... no
checking if mpiicc supports -c -o file.o... yes
checking if mpiicc supports -c -o file.o... (cached) yes
checking whether the mpiicc linker (/apps/cent7/xalt/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking whether to enable maintainer-specific portions of Makefiles... yes
checking whether we are using the GNU C++ compiler... yes
checking whether mpiicpc accepts -g... yes
checking dependency style of mpiicpc... gcc3
checking how to run the C++ preprocessor... mpiicpc -E
checking for ld used by mpiicpc... /apps/cent7/xalt/bin/ld -m elf_x86_64
checking if the linker (/apps/cent7/xalt/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the mpiicpc linker (/apps/cent7/xalt/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for mpiicpc option to produce PIC... -fPIC -DPIC
checking if mpiicpc PIC flag -fPIC -DPIC works... yes
checking if mpiicpc static flag -static works... no
checking if mpiicpc supports -c -o file.o... yes
checking if mpiicpc supports -c -o file.o... (cached) yes
checking whether the mpiicpc linker (/apps/cent7/xalt/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for g77... no
checking for xlf... no
checking for f77... no
checking for frt... no
checking for pgf77... no
checking for cf77... no
checking for fort77... no
checking for fl32... no
checking for af77... no
checking for xlf90... no
checking for f90... no
checking for pgf90... no
checking for pghpf... no
checking for epcf90... no
checking for gfortran... gfortran
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether gfortran accepts -g... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for gfortran option to produce PIC... -fPIC
checking if gfortran PIC flag -fPIC works... yes
checking if gfortran static flag -static works... no
checking if gfortran supports -c -o file.o... yes
checking if gfortran supports -c -o file.o... (cached) yes
checking whether the gfortran linker (/apps/cent7/xalt/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking how to get verbose linking output from gfortran... -v
checking for Fortran 77 libraries of gfortran... -L/home/gao477/Downloads/hdf5-1.10.5/hdf5/lib -L/home/gao477/OpenBLAS/lib -L/usr/local/lib -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/apps/cent7/intel/compilers_and_libraries_2017.1.132/linux/compiler/lib/intel64 -L/apps/cent7/intel/compilers_and_libraries_2017.1.132/linux/ipp/lib/intel64 -L/apps/cent7/intel/compilers_and_libraries_2017.1.132/linux/mkl/lib/intel64 -L/apps/cent7/intel/compilers_and_libraries_2017.1.132/linux/tbb/lib/intel64/gcc4.7 -L/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../.. -ldl -lgfortran -lm -lquadmath
checking for dummy main to link with Fortran 77 libraries... none
checking for Fortran 77 name-mangling scheme... lower case, underscore, no extra underscore
checking for OpenMP flag of C++ compiler... -fopenmp
checking for the pthreads library -lpthreads... no
checking whether pthreads work without any flags... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking if more special flags are required for pthreads... no
checking for PTHREAD_PRIO_INHERIT... yes
checking hdf5.h usability... yes
checking hdf5.h presence... yes
checking for hdf5.h... yes
checking for H5Fcreate in -lhdf5... yes
checking for H5LTmake_dataset_double in -lhdf5_hl... yes
checking for sgemm_... no
checking for ATL_xerbla in -latlas... no
checking for sgemm_ in -lblas... no
checking for sgemm_ in -lmkl... no
checking for sgemm_... (cached) no
checking for sgemm_ in -lcxml... no
checking for sgemm_ in -ldxml... no
checking for sgemm_ in -lscs... no
checking for sgemm_ in -lcomplib.sgimath... no
checking for sgemm_ in -lblas... (cached) no
checking for sgemm_ in -lblas... (cached) no
configure: error: BLAS was not found!
LD_LIBRARY_PATH defines where the libraries should be looked for at runtime, but that's the least useful information for the installation script. It needs to know where they are located during installation and mainly where the header files are located. So you need to set also LIBRARY_PATH and C_INCLUDE_PATH, roughly like this:
export LIBRARY_PATH=/home/gao477/OpenBLAS/lib:$LIBRARY_PATH
export C_INCLUDE_PATH=/home/gao477/OpenBLAS/include:$C_INCLUDE_PATH
(Don't copy that blindly, check whether the files really exist under the given paths.)
LD_LIBRARY_PATH defines where the libraries should be looked for at runtime, but that's the least useful information for the installation script. It needs to know where they are located during installation and mainly where the header files are located. So you need to set also LIBRARY_PATH and C_INCLUDE_PATH, roughly like this:
export LIBRARY_PATH=/home/gao477/OpenBLAS/lib:$LIBRARY_PATH export C_INCLUDE_PATH=/home/gao477/OpenBLAS/include:$C_INCLUDE_PATH(Don't copy that blindly, check whether the files really exist under the given paths.)
I am sorry that it still doesn't work and problem is still the same. I check the content in /OpenBLAS/lib and the files are:
cmake libopenblas_haswellp-r0.3.7.dev.a libopenblas.so pkgconfig
libopenblas.a libopenblas_haswellp-r0.3.7.dev.so libopenblas.so.0
And in the directory /OpenBLAS/include, the files are:
cblas.h lapacke_config.h lapacke_mangling.h openblas_config.h
f77blas.h lapacke.h lapacke_utils.h
I don't know whether it is right for OpenBLAS package.
I asked the similar question at the github of OpenBLAS and they told me:
"If you look at the error message carefully, it says BLAS was not found. It doesn't look for openblas at all. You should talk with the downstream projects about openblas support. (Or make a symlink libblas.so -> libopenblas.so)"
I am not very clear about the last sentence as I never used symlink before. So I tried to create a symlink with the command:
ln -s libopenblas.so libblas.so
ln -s libopenblas.a libblas.a
But it still did not work. :(
The problem is fixed by make some change of the file m4/acx_blas.m4. I added
if test $acx_blas_ok = no; then
AC_CHECK_LIB(openblas, $sgemm, [acx_blas_ok=yes;BLAS_LIBS="-lopenblas"])
fi
to this file. And it now works.
And I also link the OpenBLAS to the library:
gcc -o test test.c -I /home/gao477/packages/OpenBLAS/include -L/home/gao477/OpenBLAS/lib -lopenblas
gcc -o test test.c /home/gao477/packages/OpenBLAS/lib/libopenblas.a -lpthread -lirc
And it now works.