Open andrewsilver1997 opened 1 week ago
jwise77
commented
1 week ago I've seen this happen when there's an extra space at the end of the line in the machine file where you specify the library directories. The make system adds a /lib at the end of the given directory, and if there's a space, the lib/ append will be its own word. If this doesn't solve your problem, could you upload your machine file?
andrewsilver1997
commented
1 week ago Hi,
Thank you. The compiling process moved forward a bit but stopped at Compiling uuid/uuid_time.c. out.compile gave me the following:
/cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/binutils/2.38-GCCcore-11.3.0/bin/ld: error: /lib: read: Is a directory collect2: error: ld returned 1 exit status
My machine file is written here:
jwise77
commented
1 week ago You have to give the directory where HDF5 lives on your machine in the variable LOCAL_HDF5_INSTALL. The make system won't automatically find it for you. The same thing goes for grackle if you're using it. If HDF5 is loaded through a module on the HPC machine you're using, you can do something like which h5ls to see where it exists and remove the ending /bin and put that parent directory in your machine file.
andrewsilver1997
commented
6 days ago Hi,
Thanks for the reply. But unfortunately it still didn't work after I specified HDF5 path. This is what I did: LOCAL_HDF5_INSTALL = /cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/HDF5/1.14.3-gompi-2023b
Is there anything else I can do?
jwise77
commented
6 days ago Can you upload the original out.compile file in plain text? Also could you reupload your machine file in plain text instead of a PDF since it's easier to find any problems that way. You can use pastebin.com if it's easier for you.
andrewsilver1997
commented
6 days ago This is my out.compile: /cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/binutils/2.40-GCCcore-13.2.0/bin/ld: error: /lib: read: Is a directory collect2: error: ld returned 1 exit status
This is my makefile (Make.machine.linux-gnu):
#
#
#
#
#
#
#
#
#
#
MACH_TEXT = Generic GNU/Linux machine file. Requires gfortran/gcc/g++, OpenMPI, and a \ serial HDF5 library. Make sure to set the correct LOCAL_HDF5_INSTALL path in the \ machine file (e.g., /usr for a system-wide installation or a custom path for local \ installations). MACH_VALID = 1 MACH_FILE = Make.mach.linux-gnu
LOCAL_HDF5_INSTALL = /cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/HDF5/1.14.3-gompi-2023b # mandatory LOCAL_GRACKLE_INSTALL = /PATH/TO/GRACKLE/INSTALL # optional LOCAL_HYPRE_INSTALL = /PATH/TO/HYPRE/INSTALL # optional
MACH_CPP = cpp # C preprocessor command
MACH_CC_MPI = mpicc # C compiler when using MPI MACH_CXX_MPI = mpic++ # C++ compiler when using MPI MACH_FC_MPI = gfortran # Fortran 77 compiler when using MPI MACH_F90_MPI = gfortran # Fortran 90 compiler when using MPI MACH_LD_MPI = mpic++ # Linker when using MPI
MACH_CC_NOMPI = gcc # C compiler when not using MPI MACH_CXX_NOMPI = g++ # C++ compiler when not using MPI MACH_FC_NOMPI = gfortran # Fortran 77 compiler when not using MPI MACH_F90_NOMPI = gfortran # Fortran 90 compiler when not using MPI MACH_LD_NOMPI = g++ # Linker when not using MPI
MACH_DEFINES = -DLINUX -DH5_USE_16_API
MACH_CPPFLAGS = -P -traditional MACH_CFLAGS = MACH_CXXFLAGS = MACH_FFLAGS = -fno-second-underscore -ffixed-line-length-132 -std=legacy MACH_F90FLAGS = -fno-second-underscore -std=legacy MACH_LDFLAGS =
MACH_OPT_WARN = -Wall -g MACH_OPT_DEBUG = -g MACH_OPT_HIGH = -O2 MACH_OPT_AGGRESSIVE = -O3 -g
LOCAL_INCLUDES_MPI = # MPI includes LOCAL_INCLUDES_HDF5 = -I$(LOCAL_HDF5_INSTALL)/include # HDF5 includes LOCAL_INCLUDES_HYPRE = -I$(LOCAL_HYPRE_INSTALL)/include LOCAL_INCLUDES_PAPI = # PAPI includes LOCAL_INCLUDES_GRACKLE = -I$(LOCAL_GRACKLE_INSTALL)/include
MACH_INCLUDES = $(LOCAL_INCLUDES_HDF5) MACH_INCLUDES_MPI = $(LOCAL_INCLUDES_MPI) MACH_INCLUDES_HYPRE = $(LOCAL_INCLUDES_HYPRE) MACH_INCLUDES_PAPI = $(LOCAL_INCLUDES_PAPI) MACH_INCLUDES_GRACKLE = $(LOCAL_INCLUDES_GRACKLE)
LOCAL_LIBS_MPI = # MPI libraries LOCAL_LIBS_HDF5 = -L$(LOCAL_HDF5_INSTALL)/lib -lhdf5 -lz LOCAL_LIBS_HYPRE = -L$(LOCAL_HYPRE_INSTALL)/lib -lHYPRE LOCAL_LIBS_PAPI = # PAPI libraries LOCAL_LIBS_MACH = -lgfortran # Machine-dependent libraries LOCAL_LIBS_GRACKLE = -L$(LOCAL_GRACKLE_INSTALL)/lib -lgrackle
MACH_LIBS = $(LOCAL_LIBS_HDF5) $(LOCAL_LIBS_MACH) MACH_LIBS_MPI = $(LOCAL_LIBS_MPI) MACH_LIBS_HYPRE = $(LOCAL_LIBS_HYPRE) MACH_LIBS_PAPI = $(LOCAL_LIBS_PAPI) MACH_LIBS_GRACKLE = $(LOCAL_LIBS_GRACKLE)
Describe the bug A clear and concise description of what the bug is. I had ``make: *** [Makefile:135: enzo.exe] Error 1'' while compiling make-linux-gnu with GCCcore/11.3.0, OpenMPI/4.1.4-GCC-11.3.0, HDF5/1.12.2-gompi-2022a
when I did ``cat out.compile'', it said: /cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/software/binutils/2.38-GCCcore-11.3.0/bin/ld: error: /lib: read: Is a directory collect2: error: ld returned 1 exit status
I was running on computer cluster. And FYI, I followed the step as https://github.com/enzo-project/enzo-dev/issues/167 suggested: add -std=legacy to MACH_FFLAGS add -std=legacy to the MACH_F90FLAGS
Thank you for your help.