MBX installation

Mohsen Farshad

unread,

Sep 4, 2025, 4:07:37 PM (2 days ago) Sep 4

to MBX-users

Dear all,

The computer support at our DCC has been trying to install MBX on the system, but we encountered an error. Would you please let us know what we are missing here:

tm103@dcc-core-18 ~/storage/rhel9 $ git clone https://github.com/paesanilab/MBX.git

Cloning into 'MBX'...

remote: Enumerating objects: 20847, done.

remote: Counting objects: 100% (4168/4168), done.

remote: Compressing objects: 100% (543/543), done.

remote: Total 20847 (delta 3725), reused 3904 (delta 3595), pack-reused 16679 (from 2)

Receiving objects: 100% (20847/20847), 226.73 MiB | 26.31 MiB/s, done.

Resolving deltas: 100% (13955/13955), done.

Updating files: 100% (1273/1273), done.

tm103@dcc-core-18 ~/storage/rhel9 $ cd MBX

tm103@dcc-core-18 ~/storage/rhel9/MBX $ autoreconf -fi

aclocal: warning: couldn't open directory 'm4': No such file or directory

libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, 'build-aux'.

libtoolize: copying file 'build-aux/ltmain.sh'

libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'.

libtoolize: copying file 'm4/libtool.m4'

libtoolize: copying file 'm4/ltoptions.m4'

libtoolize: copying file 'm4/ltsugar.m4'

libtoolize: copying file 'm4/ltversion.m4'

libtoolize: copying file 'm4/lt~obsolete.m4'

configure.ac:17: installing 'build-aux/ar-lib'

configure.ac:17: installing 'build-aux/compile'

configure.ac:20: installing 'build-aux/config.guess'

configure.ac:20: installing 'build-aux/config.sub'

configure.ac:23: installing 'build-aux/install-sh'

configure.ac:23: installing 'build-aux/missing'

plugins/i-pi/Makefile.am: installing 'build-aux/depcomp'

parallel-tests: installing 'build-aux/test-driver'

tm103@dcc-core-18 ~/storage/rhel9/MBX $ ./configure --enable-mpi CXX=mpiicpc --prefix=/opt/apps/rhel9/MBX-1.3

checking for gcc... gcc

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 gcc accepts -g... yes

checking for gcc option to accept ISO C89... none needed

checking whether gcc understands -c and -o together... yes

checking for ar... ar

checking the archiver (ar) interface... ar

checking build system type... x86_64-pc-linux-gnu

checking host system type... x86_64-pc-linux-gnu

checking how to print strings... printf

checking for a sed that does not truncate output... /usr/bin/sed

checking for grep that handles long lines and -e... /usr/bin/grep

checking for egrep... /usr/bin/grep -E

checking for fgrep... /usr/bin/grep -F

checking for ld used by gcc... /usr/bin/ld

checking if the linker (/usr/bin/ld) is GNU ld... yes

checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B

checking the name lister (/usr/bin/nm -B) interface... BSD nm

checking whether ln -s works... yes

checking the maximum length of command line arguments... 1572864

checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop

checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop

checking for /usr/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 archiver @FILE support... @

checking for strip... strip

checking for ranlib... ranlib

checking for gawk... gawk

checking command to parse /usr/bin/nm -B output from gcc object... ok

checking for sysroot... no

checking for a working dd... /usr/bin/dd

checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1

checking for mt... no

checking if : is a manifest tool... no

checking how to run the C preprocessor... gcc -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 gcc supports -fno-rtti -fno-exceptions... no

checking for gcc option to produce PIC... -fPIC -DPIC

checking if gcc PIC flag -fPIC -DPIC works... yes

checking if gcc static flag -static works... no

checking if gcc supports -c -o file.o... rmdir: failed to remove 'out': Directory not empty

rm: cannot remove 'conftest/out/.nfs0000000ef525ce17000188f2': Device or resource busy

rm: cannot remove 'conftest': Is a directory

yes

checking if gcc supports -c -o file.o... (cached) yes

checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes

checking dynamic linker characteristics... rm: cannot remove 'conftest': Is a directory

rm: cannot remove 'conftest': Is a directory

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... no

checking whether to build static libraries... yes

checking for a BSD-compatible install... /usr/bin/install -c

checking whether build environment is sane... yes

checking for a thread-safe mkdir -p... /usr/bin/mkdir -p

checking whether make sets $(MAKE)... yes

checking whether make supports the include directive... yes (GNU style)

checking whether make supports nested variables... yes

checking dependency style of gcc... rm: cannot remove 'conftest.dir/sub': Directory not empty

gcc3

checking whether we are using the GNU C++ compiler... yes

checking whether mpiicpc accepts -g... yes

checking how to run the C++ preprocessor... mpiicpc -E

rm: cannot remove 'conftest': Is a directory

rm: cannot remove 'conftest.dir': Is a directory

checking for ld used by mpiicpc... /usr/bin/ld -m elf_x86_64

checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes

checking whether the mpiicpc linker (/usr/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... rmdir: failed to remove 'out': Directory not empty

rm: cannot remove 'conftest/out/.nfs0000000ef4b8791300018904': Device or resource busy

rm: cannot remove 'conftest/out/.nfs0000000ef8a8399400018903': Device or resource busy

rm: cannot remove 'conftest': Is a directory

yes

checking if mpiicpc supports -c -o file.o... (cached) yes

checking whether the mpiicpc linker (/usr/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 dependency style of mpiicpc... rm: cannot remove 'conftest.dir/sub': Directory not empty

gcc3

checking for mpiicpc option to support OpenMP... rm: cannot remove 'conftest': Is a directory

rm: cannot remove 'conftest': Is a directory

unsupported

checking for cos in -lm... rm: cannot remove 'conftest': Is a directory

rm: cannot remove 'conftest': Is a directory

no

checking for library containing omp_get_thread_num... rm: cannot remove 'conftest': Is a directory

rm: cannot remove 'conftest': Is a directory

no

configure: fftw_dir: FFTW_HOME=/opt/apps/rhel9/fftw-3.3.9/

checking for fftw_plan_dft in -lfftw3... rm: cannot remove 'conftest': Is a directory

rm: cannot remove 'conftest': Is a directory

no

configure: error: fftw3 cannot be linked. Please define FFTW_HOME.

tm103@dcc-core-18 ~/storage/rhel9/MBX $ export FFTW_HOME=/opt/apps/rhel9/fftw-3.3.9/

tm103@dcc-core-18 ~/storage/rhel9/MBX $ ./configure --enable-mpi CXX=mpiicpc --prefix=/opt/apps/rhel9/MBX-1.3

checking for gcc... gcc

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 gcc accepts -g... yes

checking for gcc option to accept ISO C89... none needed

checking whether gcc understands -c and -o together... yes

checking for ar... ar

checking the archiver (ar) interface... ar

checking build system type... x86_64-pc-linux-gnu

checking host system type... x86_64-pc-linux-gnu

checking how to print strings... printf

checking for a sed that does not truncate output... /usr/bin/sed

checking for grep that handles long lines and -e... /usr/bin/grep

checking for egrep... /usr/bin/grep -E

checking for fgrep... /usr/bin/grep -F

checking for ld used by gcc... /usr/bin/ld

checking if the linker (/usr/bin/ld) is GNU ld... yes

checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B

checking the name lister (/usr/bin/nm -B) interface... BSD nm

checking whether ln -s works... yes

checking the maximum length of command line arguments... 1572864

checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop

checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop

checking for /usr/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 archiver @FILE support... @

checking for strip... strip

checking for ranlib... ranlib

checking for gawk... gawk

checking command to parse /usr/bin/nm -B output from gcc object... ok

checking for sysroot... no

checking for a working dd... /usr/bin/dd

checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1

checking for mt... no

checking if : is a manifest tool... no

checking how to run the C preprocessor... gcc -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 gcc supports -fno-rtti -fno-exceptions... no

checking for gcc option to produce PIC... -fPIC -DPIC

checking if gcc PIC flag -fPIC -DPIC works... yes

checking if gcc static flag -static works... no

checking if gcc supports -c -o file.o... yes

checking if gcc supports -c -o file.o... (cached) yes

checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes

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... no

checking whether to build static libraries... yes

checking for a BSD-compatible install... /usr/bin/install -c

checking whether build environment is sane... yes

checking for a thread-safe mkdir -p... /usr/bin/mkdir -p

checking whether make sets $(MAKE)... yes

checking whether make supports the include directive... yes (GNU style)

checking whether make supports nested variables... yes

checking dependency style of gcc... rm: cannot remove 'conftest.dir/sub': Directory not empty

gcc3

checking whether we are using the GNU C++ compiler... yes

checking whether mpiicpc accepts -g... yes

checking how to run the C++ preprocessor... mpiicpc -E

rm: cannot remove 'conftest.dir': Is a directory

checking for ld used by mpiicpc... /usr/bin/ld -m elf_x86_64

checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes

checking whether the mpiicpc linker (/usr/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 (/usr/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 dependency style of mpiicpc... rm: cannot remove 'conftest.dir/sub': Directory not empty

gcc3

checking for mpiicpc option to support OpenMP... unsupported

checking for cos in -lm... yes

checking for library containing omp_get_thread_num... -liomp5

configure: fftw_dir: FFTW_HOME=/opt/apps/rhel9/fftw-3.3.9/

checking for fftw_plan_dft in -lfftw3... yes

checking for cblas_dgemm in -lgslcblas... yes

checking for gsl_blas_dgemm in -lgsl... yes

checking whether mpiicpc accepts -O2... yes

checking whether mpiicpc accepts -std=c++11... yes

configure: mpi_dir: none=none

checking for MPI_Init in -lmpi... yes

checking if compiler mpiicpc is able to find mpi.h... no

configure: error: compiler mpiicpc is not able to find mpi.h

tm103@dcc-core-18 ~/storage/rhel9/MBX $ source /opt/apps/rhel8/intel-2020/compilers_and_libraries/linux/mpi/intel64/bin/mpivars.sh

tm103@dcc-core-18 ~/storage/rhel9/MBX $ ./configure --enable-mpi CXX=mpiicpc --prefix=/opt/apps/rhel9/MBX-1.3

checking for gcc... gcc

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 gcc accepts -g... yes

checking for gcc option to accept ISO C89... none needed

checking whether gcc understands -c and -o together... yes

checking for ar... ar

checking the archiver (ar) interface... ar

checking build system type... x86_64-pc-linux-gnu

checking host system type... x86_64-pc-linux-gnu

checking how to print strings... printf

checking for a sed that does not truncate output... /usr/bin/sed

checking for grep that handles long lines and -e... /usr/bin/grep

checking for egrep... /usr/bin/grep -E

checking for fgrep... /usr/bin/grep -F

checking for ld used by gcc... /usr/bin/ld

checking if the linker (/usr/bin/ld) is GNU ld... yes

checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B

checking the name lister (/usr/bin/nm -B) interface... BSD nm

checking whether ln -s works... yes

checking the maximum length of command line arguments... 1572864

checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop

checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop

checking for /usr/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 archiver @FILE support... @

checking for strip... strip

checking for ranlib... ranlib

checking for gawk... gawk

checking command to parse /usr/bin/nm -B output from gcc object... ok

checking for sysroot... no

checking for a working dd... /usr/bin/dd

checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1

checking for mt... no

checking if : is a manifest tool... no

checking how to run the C preprocessor... gcc -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 gcc supports -fno-rtti -fno-exceptions... no

checking for gcc option to produce PIC... -fPIC -DPIC

checking if gcc PIC flag -fPIC -DPIC works... yes

checking if gcc static flag -static works... no

checking if gcc supports -c -o file.o... yes

checking if gcc supports -c -o file.o... (cached) yes

checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes

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... no

checking whether to build static libraries... yes

checking for a BSD-compatible install... /usr/bin/install -c

checking whether build environment is sane... yes

checking for a thread-safe mkdir -p... /usr/bin/mkdir -p

checking whether make sets $(MAKE)... yes

checking whether make supports the include directive... yes (GNU style)

checking whether make supports nested variables... yes

checking dependency style of gcc... gcc3

checking whether we are using the GNU C++ compiler... yes

checking whether mpiicpc accepts -g... yes

checking how to run the C++ preprocessor... mpiicpc -E

checking for ld used by mpiicpc... /usr/bin/ld -m elf_x86_64

checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes

checking whether the mpiicpc linker (/usr/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... rmdir: failed to remove 'out': Directory not empty

rm: cannot remove 'conftest/out/.nfs0000000ef7177f530001898f': Device or resource busy

rm: cannot remove 'conftest': Is a directory

yes

checking if mpiicpc supports -c -o file.o... (cached) yes

checking whether the mpiicpc linker (/usr/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 dependency style of mpiicpc... rm: cannot remove 'conftest.dir/sub': Directory not empty

gcc3

checking for mpiicpc option to support OpenMP... rm: cannot remove 'conftest': Is a directory

rm: cannot remove 'conftest': Is a directory

unsupported

checking for cos in -lm... rm: cannot remove 'conftest': Is a directory

rm: cannot remove 'conftest': Is a directory

no

checking for library containing omp_get_thread_num... rm: cannot remove 'conftest': Is a directory

rm: cannot remove 'conftest': Is a directory

no

configure: fftw_dir: FFTW_HOME=/opt/apps/rhel9/fftw-3.3.9/

checking for fftw_plan_dft in -lfftw3... rm: cannot remove 'conftest': Is a directory

rm: cannot remove 'conftest': Is a directory

no

configure: error: fftw3 cannot be linked. Please define FFTW_HOME.

tm103@dcc-core-18 ~/storage/rhel9/MBX $

Best,

Mohsen

Philip Zhu

unread,

Sep 4, 2025, 4:21:10 PM (2 days ago) Sep 4

to MBX-users

Hi, no promises this will solve the issue, but there are a few things you could try:

https://groups.google.com/g/mbx-users/c/SZ_v2OwcU8Q/m/4WzGUBmQCgAJ

https://groups.google.com/g/mbx-users/c/EsYhVNh0G-0/m/r3kdotpNCgAJ

Please let us know if it works or not. If it doesn't, please also attach the content of `config.log`.

Best

Henry Agnew

unread,

Sep 4, 2025, 4:32:50 PM (2 days ago) Sep 4

to MBX-users

Dear Mohsen,

Looking at your email, what stands out to me is the numerous filesystem errors such as:

rm: cannot remove 'conftest/out/.nfs0000000ef4b8791300018904': Device or resource busy

rm: cannot remove 'conftest/out/.nfs0000000ef8a8399400018903': Device or resource busy

What appears to be happening is that ./configure is attempting to run some tests, but when it tries to clean up afterwards using "rm" these filesystem errors are causing the tests to fail. These sorts of filesystem errors can have numerous causes, so you may need to consult with your supercomputer helpdesk to figure out what is causing these filesystem errors.

Have you seen these "Device or resource busy" errors before, such as when using other software?