Hello
I am trying to compile parallel MEEP on my institutions HPC cluster but am
running into an error in the configuration and make of libctl-3.2.1, when
trying to link to my compiled guile-1.8.8 library the configuration fails
to find the library and replaces guile with unknown. During the make I get
the following error:
make[2]: Entering directory `/home/php12jps/libctl-3.2.1/
utils'
/home/php12jps/libctl-3.2.1/utils/gen-ctl-io --code -o ctl-io.c ./geom.scm
..
/home/php12jps/libctl-3.2.1/utils/gen-ctl-io: line 172: unknown: command
not found
make[2]: *** [ctl-io.c] Error 1
make[2]: Leaving directory `/home/php12jps/libctl-3.2.1/utils'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/php12jps/libctl-3.2.1'
make: *** [all] Error 2
I have searched around and found the same error occurring in a macports
installation but the details of the solution were not posted:
http://www.mail-archive.com/meep-discuss@ab-initio.mit.edu/msg03661.html
I have attached the terminal output for the configuration also and was
wondering if anyone else has encountered this error or could provide some
assistance in its solution?
Thank you in advance
James
make[1]: Leaving directory `/home/php12jps/h5utils-1.12.1'
checking whether to enable maintainer-specific portions of Makefiles... no
checking for a BSD-compatible install... /usr/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 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... 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 dependency style of gcc... 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 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... 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 /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 ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
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 gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking dependency style of gcc... (cached) gcc3
checking whether gcc and cc understand -c and -o together... yes
checking for indent... indent
checking for ANSI C header files... (cached) yes
checking for guile... unknown
checking for guile-config... unknown
checking for sqrt in -lm... yes
checking for readline in -lreadline... yes
checking for dlopen in -ldl... yes
checking for gh_eval_str in -lguile... yes
checking if linking to guile works... yes
checking libguile.h usability... yes
checking libguile.h presence... yes
checking for libguile.h... yes
checking guile/gh.h usability... yes
checking guile/gh.h presence... yes
checking for guile/gh.h... yes
checking for modern non-gh interface... yes
checking for gh_enter... yes
checking for gh_eval_str... yes
checking for gh_load... yes
checking for gh_bool2scm... yes
checking for gh_vector_ref... yes
checking for gh_list_ref... yes
checking for gh_length... yes
checking for scm_flush_all_ports... yes
checking for scm_make_complex... yes
checking for scm_c_make_rectangular... yes
checking for scm_variable_set_x... yes
checking for scm_c_lookup... yes
checking for scm_c_make_vector... yes
checking for scm_variable_ref... yes
checking for SCM_COMPLEXP... yes
checking whether gh_lookup works properly... yes
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether g77 accepts -g... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
checking for g77 option to produce PIC... -fPIC
checking if g77 PIC flag -fPIC works... yes
checking if g77 static flag -static works... no
checking if g77 supports -c -o file.o... yes
checking if g77 supports -c -o file.o... (cached) yes
checking whether the g77 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 how to get verbose linking output from g77... -v
checking for Fortran 77 libraries of g77... -L/home/php12jps/local/lib
-L/usr/local/mpi/gcc/openmpi/1.6.4/lib -L/usr/local/acml-gnu2.6.0/gnu64/lib/
-L/usr/lib/gcc/x86_64-redhat-linux/3.4.6
-L/usr/lib/gcc/x86_64-redhat-linux/3.4.6/../../../../lib64
-L/usr/lib/gcc/x86_64-redhat-linux/3.4.6/../../.. -L/lib/../lib64
-L/usr/lib/../lib64 -lguile -ldl -lreadline -lfrtbegin -lg2c -lm
checking for dummy main to link with Fortran 77 libraries... none
checking for Fortran 77 name-mangling scheme... lower case, underscore, extra
underscore
checking complex.h usability... yes
checking complex.h presence... yes
checking for complex.h... yes
checking for C complex keyword... complex
checking for egrep... (cached) /bin/grep -E
checking nlopt.h usability... no
checking nlopt.h presence... no
checking for nlopt.h... no
checking for basename in -lgen... no
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating utils/Makefile
config.status: creating examples/Makefile
config.status: creating examples/example.scm
config.status: creating utils/gen-ctl-io
config.status: creating config.h
config.status: config.h is unchanged
config.status: creating src/ctl.h
config.status: src/ctl.h is unchanged
config.status: executing depfiles commands
config.status: executing libtool commands
make all-recursive
make[1]: Entering directory `/home/php12jps/libctl-3.2.1'
Making all in src
make[2]: Entering directory `/home/php12jps/libctl-3.2.1/src'
make all-am
make[3]: Entering directory `/home/php12jps/libctl-3.2.1/src'
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I..
-I/home/php12jps/local/include -O3 -I/usr/local/mpi/gcc/openmpi/1.6.4/include
-I/home/php12jps/local/include -O3 -I/usr/local/mpi/gcc/openmpi/1.6.4/include
-MT ctl.lo -MD -MP -MF .deps/ctl.Tpo -c -o ctl.lo ctl.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/php12jps/local/include
-O3 -I/usr/local/mpi/gcc/openmpi/1.6.4/include -I/home/php12jps/local/include
-O3 -I/usr/local/mpi/gcc/openmpi/1.6.4/include -MT ctl.lo -MD -MP -MF
.deps/ctl.Tpo -c ctl.c -o ctl.o
mv -f .deps/ctl.Tpo .deps/ctl.Plo
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I..
-I/home/php12jps/local/include -O3 -I/usr/local/mpi/gcc/openmpi/1.6.4/include
-I/home/php12jps/local/include -O3 -I/usr/local/mpi/gcc/openmpi/1.6.4/include
-MT subplex.lo -MD -MP -MF .deps/subplex.Tpo -c -o subplex.lo subplex.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/php12jps/local/include
-O3 -I/usr/local/mpi/gcc/openmpi/1.6.4/include -I/home/php12jps/local/include
-O3 -I/usr/local/mpi/gcc/openmpi/1.6.4/include -MT subplex.lo -MD -MP -MF
.deps/subplex.Tpo -c subplex.c -o subplex.o
mv -f .deps/subplex.Tpo .deps/subplex.Plo
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I..
-I/home/php12jps/local/include -O3 -I/usr/local/mpi/gcc/openmpi/1.6.4/include
-I/home/php12jps/local/include -O3 -I/usr/local/mpi/gcc/openmpi/1.6.4/include
-MT ctl-f77-glue.lo -MD -MP -MF .deps/ctl-f77-glue.Tpo -c -o ctl-f77-glue.lo
ctl-f77-glue.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/php12jps/local/include
-O3 -I/usr/local/mpi/gcc/openmpi/1.6.4/include -I/home/php12jps/local/include
-O3 -I/usr/local/mpi/gcc/openmpi/1.6.4/include -MT ctl-f77-glue.lo -MD -MP -MF
.deps/ctl-f77-glue.Tpo -c ctl-f77-glue.c -o ctl-f77-glue.o
mv -f .deps/ctl-f77-glue.Tpo .deps/ctl-f77-glue.Plo
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I..
-I/home/php12jps/local/include -O3 -I/usr/local/mpi/gcc/openmpi/1.6.4/include
-I/home/php12jps/local/include -O3 -I/usr/local/mpi/gcc/openmpi/1.6.4/include
-MT integrator.lo -MD -MP -MF .deps/integrator.Tpo -c -o integrator.lo
integrator.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/php12jps/local/include
-O3 -I/usr/local/mpi/gcc/openmpi/1.6.4/include -I/home/php12jps/local/include
-O3 -I/usr/local/mpi/gcc/openmpi/1.6.4/include -MT integrator.lo -MD -MP -MF
.deps/integrator.Tpo -c integrator.c -o integrator.o
mv -f .deps/integrator.Tpo .deps/integrator.Plo
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I..
-I/home/php12jps/local/include -O3 -I/usr/local/mpi/gcc/openmpi/1.6.4/include
-I/home/php12jps/local/include -O3 -I/usr/local/mpi/gcc/openmpi/1.6.4/include
-MT cintegrator.lo -MD -MP -MF .deps/cintegrator.Tpo -c -o cintegrator.lo
cintegrator.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/php12jps/local/include
-O3 -I/usr/local/mpi/gcc/openmpi/1.6.4/include -I/home/php12jps/local/include
-O3 -I/usr/local/mpi/gcc/openmpi/1.6.4/include -MT cintegrator.lo -MD -MP -MF
.deps/cintegrator.Tpo -c cintegrator.c -o cintegrator.o
mv -f .deps/cintegrator.Tpo .deps/cintegrator.Plo
/bin/sh ../libtool --tag=CC --mode=link gcc -I/home/php12jps/local/include
-O3 -I/usr/local/mpi/gcc/openmpi/1.6.4/include -no-undefined -version-info
5:1:0 -L/home/php12jps/local/lib -L/usr/local/mpi/gcc/openmpi/1.6.4/lib
-L/usr/local/acml-gnu2.6.0/gnu64/lib/ -o libctl.la -rpath
/home/php12jps/local/lib ctl.lo subplex.lo ctl-f77-glue.lo integrator.lo
cintegrator.lo -lguile -ldl -lreadline -lm
libtool: link: rm -fr .libs/libctl.a .libs/libctl.la .libs/libctl.lai
libtool: link: ar cru .libs/libctl.a ctl.o subplex.o ctl-f77-glue.o
integrator.o cintegrator.o
libtool: link: ranlib .libs/libctl.a
libtool: link: ( cd ".libs" && rm -f "libctl.la" && ln -s "../libctl.la"
"libctl.la" )
make[3]: Leaving directory `/home/php12jps/libctl-3.2.1/src'
make[2]: Leaving directory `/home/php12jps/libctl-3.2.1/src'
Making all in utils
make[2]: Entering directory `/home/php12jps/libctl-3.2.1/utils'
/home/php12jps/libctl-3.2.1/utils/gen-ctl-io --code -o ctl-io.c ./geom.scm ..
/home/php12jps/libctl-3.2.1/utils/gen-ctl-io: line 172: unknown: command not
found
make[2]: *** [ctl-io.c] Error 1
make[2]: Leaving directory `/home/php12jps/libctl-3.2.1/utils'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/php12jps/libctl-3.2.1'
make: *** [all] Error 2
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