[BUG]collect2: error: ld returned 1 exit status

[andrewsilver1997]

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 #167 suggested:
add -std=legacy to MACH_FFLAGS
add -std=legacy to the MACH_F90FLAGS

Thank you for your help.

[jwise77]

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]

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:

Make.mach.linux-gnu.pdf

[jwise77]

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]

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]

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]

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):
#=======================================================================

FILE: Make.mach.linux-gnu

DESCRIPTION: Makefile settings for a linux machine

AUTHOR: Rick Wagner (rick@ucsd.edu)

DATE: 2008-09-16 (updated 2019-09-11)

Depending on your linux distribution several packages need to be installed

to satisfy the minimum Enzo requirements (GNU compiler suite with

gfortran/gcc/g++, an MPI library for parallel runs, and HDF5 for data outputs).

Sample environments

Ubuntu/Debian (see also Make.mach.ubuntu):

$ apt-get install build-essentials gfortran libhdf5-10 libopenmpi-dev openmpi-bin

Fedora/Redhat:

$ yum install make automake gcc gcc-c++ gcc-gfortran kernel-devel openmpi openmpi-devel

Arch Linux:

$ pacman -S base-devel gcc-fortran openmpi hdf5

#=======================================================================

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

#-----------------------------------------------------------------------

Install paths (local variables)

#-----------------------------------------------------------------------

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

#-----------------------------------------------------------------------

Compiler settings

#-----------------------------------------------------------------------

MACH_CPP = cpp # C preprocessor command

With MPI

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

Without 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

#-----------------------------------------------------------------------

Machine-dependent defines

#-----------------------------------------------------------------------

MACH_DEFINES = -DLINUX -DH5_USE_16_API

#-----------------------------------------------------------------------

Compiler flag settings

#-----------------------------------------------------------------------

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 =

#-----------------------------------------------------------------------

Optimization flags

#-----------------------------------------------------------------------

MACH_OPT_WARN = -Wall -g
MACH_OPT_DEBUG = -g
MACH_OPT_HIGH = -O2
MACH_OPT_AGGRESSIVE = -O3 -g

#-----------------------------------------------------------------------

Includes

#-----------------------------------------------------------------------

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)

#-----------------------------------------------------------------------

Libraries

#-----------------------------------------------------------------------

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)