necpp
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Published
20 hours ago •
tmolteno
tmolteno
clapack.h not found
In Ubuntu 16.04 LTS, with properly intalled g++, make, automake, autoconf, libtool and libatlas-base-dev compilation will fail at:
matrix_algebra.cpp:412:21: fatal error: clapack.h: File or directory not found
Hi @mhdry , Can you please post the ouput of the configure and build here?
Also please check the location of clapack.h. The .h file should be in /usr/include/atlas. Therefore, the configure and make should include this location.
In the output it should say like
ATLAS_INCLUDE_DIR = /usr/include/atlas
If not then you have found your error.
Please tell what happens so that it can be fixed.
There is
-rw-r--r-- 1 root root 9708 Nov 24 2015 /usr/include/atlas/clapack.h
on my system, but I can't see ATLAS_INCLUDE_DIR = /usr/include/atlas in any of the output:
(1) make -f Makefile.git
libtoolize --force --copy
libtoolize: putting auxiliary files in '.'.
libtoolize: copying file './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'
aclocal
autoheader
automake --add-missing
configure.ac:6: installing './compile'
configure.ac:6: installing './config.guess'
configure.ac:6: installing './config.sub'
configure.ac:4: installing './install-sh'
configure.ac:4: installing './missing'
src/Makefile.am: installing './depcomp'
autoconf
(2) ./configure CXX=g++-5 CXXFLAGS="-O2 -march=nocona -pipe"
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 whether make supports nested variables... yes
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 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 whether gcc understands -c and -o together... yes
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... 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 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 a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... mt
checking if mt 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... yes
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 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 for date... /bin/date
configure: Build date: 2018-02-27
checking for clapack_zgetrf in -llapack... yes
checking whether we are using the GNU C++ compiler... yes
checking whether g++-5 accepts -g... yes
checking dependency style of g++-5... gcc3
checking how to run the C++ preprocessor... g++-5 -E
checking for ld used by g++-5... /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 g++-5 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for g++-5 option to produce PIC... -fPIC -DPIC
checking if g++-5 PIC flag -fPIC -DPIC works... yes
checking if g++-5 static flag -static works... yes
checking if g++-5 supports -c -o file.o... yes
checking if g++-5 supports -c -o file.o... (cached) yes
checking whether the g++-5 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 for pow in -lm... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating necpp.pc
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
(3) make -j 4
make all-recursive
make[1]: Verzeichnis „/home/user/necpp“ wird betreten
Making all in src
make[2]: Verzeichnis „/home/user/necpp/src“ wird betreten
/bin/bash ../libtool --tag=CXX --mode=compile g++-5 -DHAVE_CONFIG_H -I. -I.. -O2 -g0 -Wall -Wextra -Wshadow -Wconversion -O2 -march=nocona -pipe -MT libnecpp_la-c_evlcom.lo -MD -MP -MF .deps/libnecpp_la-c_evlcom.Tpo -c -o libnecpp_la-c_evlcom.lo `test -f 'c_evlcom.cpp' || echo './'`c_evlcom.cpp
/bin/bash ../libtool --tag=CXX --mode=compile g++-5 -DHAVE_CONFIG_H -I. -I.. -O2 -g0 -Wall -Wextra -Wshadow -Wconversion -O2 -march=nocona -pipe -MT libnecpp_la-c_geometry.lo -MD -MP -MF .deps/libnecpp_la-c_geometry.Tpo -c -o libnecpp_la-c_geometry.lo `test -f 'c_geometry.cpp' || echo './'`c_geometry.cpp
/bin/bash ../libtool --tag=CXX --mode=compile g++-5 -DHAVE_CONFIG_H -I. -I.. -O2 -g0 -Wall -Wextra -Wshadow -Wconversion -O2 -march=nocona -pipe -MT libnecpp_la-c_ggrid.lo -MD -MP -MF .deps/libnecpp_la-c_ggrid.Tpo -c -o libnecpp_la-c_ggrid.lo `test -f 'c_ggrid.cpp' || echo './'`c_ggrid.cpp
/bin/bash ../libtool --tag=CXX --mode=compile g++-5 -DHAVE_CONFIG_H -I. -I.. -O2 -g0 -Wall -Wextra -Wshadow -Wconversion -O2 -march=nocona -pipe -MT libnecpp_la-c_plot_card.lo -MD -MP -MF .deps/libnecpp_la-c_plot_card.Tpo -c -o libnecpp_la-c_plot_card.lo `test -f 'c_plot_card.cpp' || echo './'`c_plot_card.cpp
libtool: compile: g++-5 -DHAVE_CONFIG_H -I. -I.. -O2 -g0 -Wall -Wextra -Wshadow -Wconversion -O2 -march=nocona -pipe -MT libnecpp_la-c_evlcom.lo -MD -MP -MF .deps/libnecpp_la-c_evlcom.Tpo -c c_evlcom.cpp -fPIC -DPIC -o .libs/libnecpp_la-c_evlcom.o
libtool: compile: g++-5 -DHAVE_CONFIG_H -I. -I.. -O2 -g0 -Wall -Wextra -Wshadow -Wconversion -O2 -march=nocona -pipe -MT libnecpp_la-c_ggrid.lo -MD -MP -MF .deps/libnecpp_la-c_ggrid.Tpo -c c_ggrid.cpp -fPIC -DPIC -o .libs/libnecpp_la-c_ggrid.o
libtool: compile: g++-5 -DHAVE_CONFIG_H -I. -I.. -O2 -g0 -Wall -Wextra -Wshadow -Wconversion -O2 -march=nocona -pipe -MT libnecpp_la-c_geometry.lo -MD -MP -MF .deps/libnecpp_la-c_geometry.Tpo -c c_geometry.cpp -fPIC -DPIC -o .libs/libnecpp_la-c_geometry.o
libtool: compile: g++-5 -DHAVE_CONFIG_H -I. -I.. -O2 -g0 -Wall -Wextra -Wshadow -Wconversion -O2 -march=nocona -pipe -MT libnecpp_la-c_plot_card.lo -MD -MP -MF .deps/libnecpp_la-c_plot_card.Tpo -c c_plot_card.cpp -fPIC -DPIC -o .libs/libnecpp_la-c_plot_card.o
libtool: compile: g++-5 -DHAVE_CONFIG_H -I. -I.. -O2 -g0 -Wall -Wextra -Wshadow -Wconversion -O2 -march=nocona -pipe -MT libnecpp_la-c_plot_card.lo -MD -MP -MF .deps/libnecpp_la-c_plot_card.Tpo -c c_plot_card.cpp -o libnecpp_la-c_plot_card.o >/dev/null 2>&1
mv -f .deps/libnecpp_la-c_plot_card.Tpo .deps/libnecpp_la-c_plot_card.Plo
/bin/bash ../libtool --tag=CXX --mode=compile g++-5 -DHAVE_CONFIG_H -I. -I.. -O2 -g0 -Wall -Wextra -Wshadow -Wconversion -O2 -march=nocona -pipe -MT libnecpp_la-libNEC.lo -MD -MP -MF .deps/libnecpp_la-libNEC.Tpo -c -o libnecpp_la-libNEC.lo `test -f 'libNEC.cpp' || echo './'`libNEC.cpp
libtool: compile: g++-5 -DHAVE_CONFIG_H -I. -I.. -O2 -g0 -Wall -Wextra -Wshadow -Wconversion -O2 -march=nocona -pipe -MT libnecpp_la-c_ggrid.lo -MD -MP -MF .deps/libnecpp_la-c_ggrid.Tpo -c c_ggrid.cpp -o libnecpp_la-c_ggrid.o >/dev/null 2>&1
libtool: compile: g++-5 -DHAVE_CONFIG_H -I. -I.. -O2 -g0 -Wall -Wextra -Wshadow -Wconversion -O2 -march=nocona -pipe -MT libnecpp_la-libNEC.lo -MD -MP -MF .deps/libnecpp_la-libNEC.Tpo -c libNEC.cpp -fPIC -DPIC -o .libs/libnecpp_la-libNEC.o
libtool: compile: g++-5 -DHAVE_CONFIG_H -I. -I.. -O2 -g0 -Wall -Wextra -Wshadow -Wconversion -O2 -march=nocona -pipe -MT libnecpp_la-c_evlcom.lo -MD -MP -MF .deps/libnecpp_la-c_evlcom.Tpo -c c_evlcom.cpp -o libnecpp_la-c_evlcom.o >/dev/null 2>&1
mv -f .deps/libnecpp_la-c_ggrid.Tpo .deps/libnecpp_la-c_ggrid.Plo
/bin/bash ../libtool --tag=CXX --mode=compile g++-5 -DHAVE_CONFIG_H -I. -I.. -O2 -g0 -Wall -Wextra -Wshadow -Wconversion -O2 -march=nocona -pipe -MT libnecpp_la-matrix_algebra.lo -MD -MP -MF .deps/libnecpp_la-matrix_algebra.Tpo -c -o libnecpp_la-matrix_algebra.lo `test -f 'matrix_algebra.cpp' || echo './'`matrix_algebra.cpp
libtool: compile: g++-5 -DHAVE_CONFIG_H -I. -I.. -O2 -g0 -Wall -Wextra -Wshadow -Wconversion -O2 -march=nocona -pipe -MT libnecpp_la-libNEC.lo -MD -MP -MF .deps/libnecpp_la-libNEC.Tpo -c libNEC.cpp -o libnecpp_la-libNEC.o >/dev/null 2>&1
libtool: compile: g++-5 -DHAVE_CONFIG_H -I. -I.. -O2 -g0 -Wall -Wextra -Wshadow -Wconversion -O2 -march=nocona -pipe -MT libnecpp_la-matrix_algebra.lo -MD -MP -MF .deps/libnecpp_la-matrix_algebra.Tpo -c matrix_algebra.cpp -fPIC -DPIC -o .libs/libnecpp_la-matrix_algebra.o
matrix_algebra.cpp:412:21: fatal error: clapack.h: Datei oder Verzeichnis nicht gefunden
compilation terminated.
Makefile:673: die Regel für Ziel „libnecpp_la-matrix_algebra.lo“ scheiterte
make[2]: *** [libnecpp_la-matrix_algebra.lo] Fehler 1
make[2]: *** Auf noch nicht beendete Prozesse wird gewartet …
mv -f .deps/libnecpp_la-c_evlcom.Tpo .deps/libnecpp_la-c_evlcom.Plo
mv -f .deps/libnecpp_la-libNEC.Tpo .deps/libnecpp_la-libNEC.Plo
libtool: compile: g++-5 -DHAVE_CONFIG_H -I. -I.. -O2 -g0 -Wall -Wextra -Wshadow -Wconversion -O2 -march=nocona -pipe -MT libnecpp_la-c_geometry.lo -MD -MP -MF .deps/libnecpp_la-c_geometry.Tpo -c c_geometry.cpp -o libnecpp_la-c_geometry.o >/dev/null 2>&1
mv -f .deps/libnecpp_la-c_geometry.Tpo .deps/libnecpp_la-c_geometry.Plo
make[2]: Verzeichnis „/home/user/necpp/src“ wird verlassen
Makefile:470: die Regel für Ziel „all-recursive“ scheiterte
make[1]: *** [all-recursive] Fehler 1
make[1]: Verzeichnis „/home/user/necpp“ wird verlassen
Makefile:379: die Regel für Ziel „all“ scheiterte
make: *** [all] Fehler 2
Ubuntu 18.04, no clapack.h at all after installing libatlas-base-dev libatlas3-base. After installing anything containing "libatlas" i.e. apt install libatlas*, clapack.h can be found in /usr/include/x86_64-linux-gnu/clapack.h. Yet, some applications can not find it there.
Hi,
I faced the same problem, this is the work around which worked for me:
CXXFLAGS=-I<path> and CFLAGS=-I<path>
where clapack.h include file.
I didn't see any configure option which lets you specify the atlas build location.
on ubuntu 20.04 clapack.h is located at
/usr/include/x86_64-linux-gnu libs at /usr/lib/x86_64-linux-gnu
