I'm working on implementing a user subroutine for LS-DYNA in linux Red Hat 5.11. To implement the subroutine an executable object file needs to be complied that includes the subroutine fortran code. I have a makefile that needs to be executed to create the .o file.
The problem is that the makefile was written for the Intel Fortran compiler but I only have assess to GFortran. I've already switched the compiler directory but I'm unsure what the other compiler commands do and how to execute those in GFortran. Here's the makefile:
lsdyna: dyn21.o dyn21b.o couple2other_user.o
/usr/bin/gfortran -o lsdyna init_once.o init_keywrd.o dynm.o dyn21.o dyn21b.o couple2other_user.o adummy_graph.o orderByMetis.o adummy_msc.o mscapi.o libdyna.a libbcsext4.a liblsda.a liblssecurity.a liblcpack.a libspooles.a libcparse.a libmf2.a liblsm.a liblscrypt.a libresurf.a libsfg.a libmetis.a libfemster_wrap.a libfemster_wrap2d.a libfemster_wrap1d.a libfemster.a libfemster2d.a libfemster1d.a libpfem.a libmetis.a libblas.a liblapack.a libfftw3.a libsprng.a intel64_101_libansysdp.a libdyna.a libblas.a liblapack.a libmetis.a -i-static -L/usr/X11R6/lib64 -lX11 -openmp -lstdc++ -lrt -lstdc++
dyn21.o: dyn21.f nhisparm.inc
/usr/bin/gfortran -c -w95 -zero -assume byterecl,buffered_io,protect_parens -mP2OPT_hpo_dist_factor=21 -ftz -nopad -fpp2 -openmp -i8 -r8 -DINTEL -DAdd_ -xW -fp-model precise -O2 -I. dyn21.f
dyn21b.o: dyn21b.f nhisparm.inc
/usr/bin/gfortran -c -w95 -zero -assume byterecl,buffered_io,protect_parens -mP2OPT_hpo_dist_factor=21 -ftz -nopad -fpp2 -openmp -i8 -r8 -DINTEL -DAdd_ -xW -fp-model precise -O2 -I. dyn21b.f
couple2other_user.o: couple2other_user.f
/usr/bin/gfortran -c -w95 -zero -assume byterecl,buffered_io,protect_parens -mP2OPT_hpo_dist_factor=21 -ftz -nopad -fpp2 -openmp -i8 -r8 -DINTEL -DAdd_ -xW -fp-model precise -O2 -I. couple2other_user.f
Related
Info:
Linux watvde0453 3.10.0-1062.1.1.el7.x86_64 #1 SMP Fri Sep 13 22:55:44 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
GNU Make 4.2.1
Built for x86_64-pc-linux-gnu
Hi
I have been playing around with a make file to allow builds of shared, static libraries and an exe (and also to get some sort of understanding about how it works) and came across some behavior I do not understand.
I was trying to separate out the flags used for lib / exe into separate variables, but when using a line to compile and link all in one it looks like only the CFLAGS variable is being included for the compile step.
When using the following makefile:
LIBCFLAGS := -fPIC
CFLAGS := -O3 -g -Wall -Werror
CC := gcc
SRCS=hashfunction.c hashtable.c hashtablelinkedlist.c
OBJS=hashfunction.o hashtable.o hashtablelinkedlist.o
LIBSO = lib$(NAME).so
libso: $(OBJS)
$(CC) $(LIBCFLAGS) $(CFLAGS) -shared -o $(LIBSO) $(OBJS)
I get the following output when running the make command for libso:
$ make libso
gcc -O3 -g -Wall -Werror -c -o hashfunction.o hashfunction.c
gcc -O3 -g -Wall -Werror -c -o hashtable.o hashtable.c
gcc -O3 -g -Wall -Werror -c -o hashtablelinkedlist.o hashtablelinkedlist.c
gcc -fPIC -O3 -g -Wall -Werror -shared -o lib.so hashfunction.o hashtable.o hashtablelinkedlist.o
/tools/oss/packages/x86_64-centos7/binutils/default/bin/ld: hashtable.o: relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a shared object; recompile with -fPIC
hashtable.o: error adding symbols: Bad value
collect2: error: ld returned 1 exit status
make: *** [Makefile:12: libso] Error 1
I can get it all working by sticking all the flags in CFLAGS, but I was wondering if anyone could explain what make is doing underneath ?
It looks like the $(LIBCFLAGS) is being ignored for the implicit compile lines, but $(CFLAGS) is not. Is CFALGS used implicitly by make for all compilations ?
You can see all the built-in rules make knows about by running make -p -f/dev/null. There you'll see:
%.o: %.c
# recipe to execute (built-in):
$(COMPILE.c) $(OUTPUT_OPTION) $<
which is the built-in rule make uses to create a .o file from a .c file. Looking elsewhere in the output you'll see:
COMPILE.c = $(CC) $(CFLAGS) $(CPPFLAGS) $(TARGET_ARCH) -c
so these are the variables make uses to compile .c files into .o files.
I am trying to compile til parameter estimation tool PEST (http://www.pesthomepage.org/) for linux.
According to the PEST-manual I did:
make -f pest.mak all
but I get following error message:
gfortran -c -O3 -static pestdata.for
gfortran -c -O3 -static pest.for
gfortran -c -O3 -static pestsub2.for
gfortran -c -O3 -static writall.for
gfortran -c -O3 -static pardef.for
gfortran -c -O3 -static readpest.for
gfortran -c -O3 -static runpest.for
gfortran -static -o pest \
pest.o pestsub1.o pestsub2.o dercalc.o modrun.o writall.o \
linpos.o lapack1.o writsig.o common.o \
pgetcl.o pestwait.o writint.o pardef.o\
drealrd.o space.o optwt.o cgsolve.o compress.o \
readpest.o runpest.o lsqr.o orthog.o ms_stubs.o pestdata.o
/bin/ld: cannot find -lgfortran
/bin/ld: cannot find -lm
/bin/ld: cannot find -lquadmath
/bin/ld: cannot find -lm
/bin/ld: cannot find -lc
collect2: error: ld returned 1 exit status
make: *** [pest] Error 1
After goggling I have tried different things, but without results. Can somebody please help
me?
Regards Tanja
Solutions to a problem shouldn't be hidden in comments, which is why I write this answer.
The make output shows that the Makefile tries to link statically.
That requires the libraries that can be linked statically, notably libm.a, libgfortran.a, libquadmath.a and libc.a
A possible solution is to remove the -static flag in the final step.
The resulting executable will of course need the shared objects (libm.so and friends) in order to be able to run. In most situations that's not a problem though.
I am trying to write a makefile that I can use on linux and mac that builds with an address sanitizer. This works on my vagrant instance:
CC = gcc
ASAN_FLAGS = -fsanitize=address -fno-omit-frame-pointer -Wno-format-security
ASAN_LIBS = -static-libasan
CFLAGS := -Wall -Werror --std=gnu99 -g3
LDFLAGS += -lpthread
all: hello
hello: tiny_queue.o hello.o
$(CC) -o $# $(CFLAGS) $(ASAN_FLAGS) $(CURL_CFLAGS) $^ $(LDFLAGS) $(CURL_LIBS) $(ASAN_LIBS)
This works on ubuntu/trusty64 but fails on my mac with
$ make
gcc -Wall -Werror --std=gnu99 -g3 -I/opt/X11/include -c -o hello.o hello.c
gcc -o hello -Wall -Werror --std=gnu99 -g3 -fsanitize=address -fno-omit-frame-pointer -Wno-format-security tiny_queue.o hello.o -lpthread -static-libasan
clang: error: unknown argument: '-static-libasan'
make: *** [hello] Error 1
Does anyone know how to write a compatible makefile for the mac and linux?
p.s. I'm very new to C, sorry if this question is super basic.
CC = gcc
ASAN_FLAGS = -fsanitize=address -fno-omit-frame-pointer -Wno-format-security
ASAN_LIBS = -static-libasan
CFLAGS := -Wall -Werror --std=gnu99 -g3
LDFLAGS += -lpthread
all: hello
hello: tiny_queue.o hello.o
$(CC) -o $# $(CFLAGS) $(ASAN_FLAGS) $(CURL_CFLAGS) $^ $(LDFLAGS) $(CURL_LIBS) $(ASAN_LIBS)
You should not specify an Asan library (or a UBsan library, for that matter). Since you are using the compiler driver to drive link, just use -fsanitize=address (this is the recommended way of doing it). Do not add -static-libasan. The compiler driver will add the proper libraries for you.
I built libssl.a and libcryto.a. But when I want to link my.so to it, I got this error:
Error:(130) undefined reference to 'BIO_new_dgram'
If I delete this call, I can compile it succeed.
Did I build the library of openssl in a wrong way?
BIO_new_dgram is in libcrypto.a:
nm libcrypto.a | grep BIO_new_dgram
0000081c T BIO_new_dgram
I configure Openssl with:
./config shared --openssldir=$install_dir --prefix=$install_dir
and link command:
/home/choury/bin/Android/android-sdk-linux/ndk-bundle/toolchains/llvm/prebuilt/l
inux-x86_64/bin/clang++ --target=aarch64-none-linux-android --gcc-toolchain=/ho
me/choury/bin/Android/android-sdk-linux/ndk-bundle/toolchains/aarch64-linux-andr
oid-4.9/prebuilt/linux-x86_64 --sysroot=/home/choury/bin/Android/android-sdk-lin
ux/ndk-bundle/platforms/android-21/arch-arm64 -fPIC -std=c++11 -Wall -fPIC -ggdb
-O0 -Wl,--build-id -Wl,--warn-shared-textrel -Wl,--fatal-warnings -Wl,--no-und
efined -Wl,-z,noexecstack -Qunused-arguments -Wl,-z,relro -Wl,-z,now -Wl,--build
-id -Wl,--warn-shared-textrel -Wl,--fatal-warnings -Wl,--no-undefined -Wl,-z,noe
xecstack -Qunused-arguments -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,my.so -o
$outpath/my.so $mypath/a.o $mypath/b.o $install_dir/lib/libssl.a $install_dir/li
b/libcrypto.a -ldl my.a -lz -llog -lm "/home/choury/bin/Android/android-sdk-linux
/ndk-bundle/sources/cxx-stl/gnu-libstdc++/4.9/libs/arm64-v8a/libsupc++.a" "/home/
choury/bin/Android/android-sdk-linux/ndk-bundle/sources/cxx-stl/gnu-libstdc++/4.9
/libs/arm64-v8a/libgnustl_shared.so"
I build the project with cmake, the Openssl part of it:
set(OPENSSL_INCLUDE_DIR ${OPENSSL_ROOT_DIR}/include)
set(OPENSSL_LIBRARIES ${OPENSSL_ROOT_DIR}/lib)
set(OPENSSL_CRYPTO_LIBRARY ${OPENSSL_LIBRARIES}/libcrypto.a)
set(OPENSSL_SSL_LIBRARY ${OPENSSL_LIBRARIES}/libssl.a)
find_package(OpenSSL REQUIRED IMPORTED)
The OPENSSL_ROOT_DIR is set with $install_dir in build.gradle.
The linker in NDK is sensitive to the order of static libraries on command line. If libA.a depends on libB.a, the command line should be
clang++ … a.o b.o a/libA.a b/libB.a … -Llibs -lm -ldl -lz -llog -o libqq.so
here I assume libm.so, libdl.so, libz.so and liblog.so. Note that the following command is equivalent:
clang++ … a.o b.o -La -lA -Lb -lB … -Llibs -lm -ldl -lz -llog -o libqq.so
I am working with the ARM-gcc cross compiler and am having issues linking to any implementation within libc.
Compiling prog.c, writing to prog.o...
~/.programs/arm-gcc/bin/arm-none-eabi-gcc -Wall -fno-common -mcpu=cortex-m4 -mthumb -O0 -g -DF_CPU=72000000 -I~/.programs/arm-gcc/arm-none-eabi/include -I../include -I. -I../src/include -c prog.c -o prog.o > prog.lst
Compiling ../common/sysinit.c, writing to sysinit.o...
~/.programs/arm-gcc/bin/arm-none-eabi-gcc -Wall -fno-common -mcpu=cortex-m4 -mthumb -O0 -g -DF_CPU=72000000 -I~/.programs/arm-gcc/arm-none-eabi/include -I../include -I. -I../src/include -c ../common/sysinit.c -o sysinit.o > sysinit.lst
Assembling ../common/crt0.s, writing to crt0.o...
~/.programs/arm-gcc/bin/arm-none-eabi-as -mcpu=cortex-m4 -o crt0.o ../common/crt0.s > crt0.lst
Compiling uart.c, writing to uart.o...
~/.programs/arm-gcc/bin/arm-none-eabi-gcc -Wall -fno-common -mcpu=cortex-m4 -mthumb -O0 -g -DF_CPU=72000000 -I~/.programs/arm-gcc/arm-none-eabi/include -I../include -I. -I../src/include -c uart.c -o uart.o > uart.lst
~/.programs/arm-gcc/bin/arm-none-eabi-ld prog.o sysinit.o crt0.o uart.o -Map=prog.map -T../common/Teensy31_flash.ld -L~/.programs/arm-gcc/arm-none-eabi/lib -o prog.elf
prog.o: In function `print_char':
/home/user/workspace/prog/src/prog.c:47: undefined reference to `sprintf'
/home/user/workspace/prog/src/prog.c:48: undefined reference to `printf'
/home/user/workspace/prog/src/prog.c:49: undefined reference to `strlen'
prog.o: In function `main':
/home/user/workspace/prog/src/prog.c:72: undefined reference to `memset'
make: *** [makefile:133: prog.elf] Error 1
I threw in a few calls to stdlib to make the point. I have tried to explicitly link against libc using -lc but am met with:
/home/prog/.programs/arm-gcc/bin/arm-none-eabi-ld: cannot find -lc
The archive directory is passed to the linker via:
L~/.programs/arm-gcc/arm-none-eabi/lib
I have checked the contents of this directory and verified the archive to be present:
$ ls ~/.programs/arm-gcc/arm-none-eabi/lib
aprofile-validation.specs libc_s.a linux.specs
aprofile-ve.specs libg.a nano.specs
armv6-m libgloss-linux.a nosys.specs
armv7-ar libg_s.a pid.specs
armv7e-m libm.a rdimon-crt0.o
armv7-m libnosys.a rdimon.specs
cpu-init librdimon.a rdpmon-crt0.o
crt0.o librdimon_s.a rdpmon.specs
fpu librdpmon.a redboot-crt0.o
iq80310.specs libstdc++.a redboot.ld
ldscripts libstdc++.a-gdb.py redboot.specs
libarm_cortexM0l_math.a libstdc++_s.a redboot-syscalls.o
libarm_cortexM4lf_math.a libsupc++.a thumb
libarm_cortexM4l_math.a libsupc++_s.a
libc.a linux-crt0.o
And, finally, the libc does export sprintf (and others)
$ nm libc.a | grep "sprintf"
...
lib_a-sprintf.o:
00000000 T sprintf
00000000 T _sprintf_r
U sprintf
U _sprintf_r
...
Info on the ARM-GCC build I am using:
$ ./arm-none-eabi-gcc -v
Using built-in specs.
COLLECT_GCC=./arm-none-eabi-gcc
COLLECT_LTO_WRAPPER=/home/user/.programs/arm-gcc/bin/../lib/gcc/arm-none-eabi/5.4.1/lto-wrapper
Target: arm-none-eabi
Configured with: /home/build/work/GCC-5-0-build/src/gcc/configure --target=arm-none-eabi --prefix=/home/build/work/GCC-5-0-build/install-native --libexecdir=/home/build/work/GCC-5-0-build/install-native/lib --infodir=/home/build/work/GCC-5-0-build/install-native/share/doc/gcc-arm-none-eabi/info --mandir=/home/build/work/GCC-5-0-build/install-native/share/doc/gcc-arm-none-eabi/man --htmldir=/home/build/work/GCC-5-0-build/install-native/share/doc/gcc-arm-none-eabi/html --pdfdir=/home/build/work/GCC-5-0-build/install-native/share/doc/gcc-arm-none-eabi/pdf --enable-languages=c,c++ --enable-plugins --disable-decimal-float --disable-libffi --disable-libgomp --disable-libmudflap --disable-libquadmath --disable-libssp --disable-libstdcxx-pch --disable-nls --disable-shared --disable-threads --disable-tls --with-gnu-as --with-gnu-ld --with-newlib --with-headers=yes --with-python-dir=share/gcc-arm-none-eabi --with-sysroot=/home/build/work/GCC-5-0-build/install-native/arm-none-eabi --build=i686-linux-gnu --host=i686-linux-gnu --with-gmp=/home/build/work/GCC-5-0-build/build-native/host-libs/usr --with-mpfr=/home/build/work/GCC-5-0-build/build-native/host-libs/usr --with-mpc=/home/build/work/GCC-5-0-build/build-native/host-libs/usr --with-isl=/home/build/work/GCC-5-0-build/build-native/host-libs/usr --with-cloog=/home/build/work/GCC-5-0-build/build-native/host-libs/usr --with-libelf=/home/build/work/GCC-5-0-build/build-native/host-libs/usr --with-host-libstdcxx='-static-libgcc -Wl,-Bstatic,-lstdc++,-Bdynamic -lm' --with-pkgversion='GNU Tools for ARM Embedded Processors' --with-multilib-list=armv6-m,armv7-m,armv7e-m,armv7-r,armv8-m.base,armv8-m.main
Thread model: single
gcc version 5.4.1 20160609 (release) [ARM/embedded-5-branch revision 237715] (GNU Tools for ARM Embedded Processors)
The ~ in -L~/.programs/arm-gcc/arm-none-eabi/lib doesn't get expanded. It is the shell that expands ~ into /home/user, but only when it is at the beginning of a word.
Actually, it isn't necessary to add this -L option, because this is already in gcc's default search path. However, you link directly with ld instead of with gcc. That is not a good idea. It is better to link with gcc and allow it to add the default search paths and other required libraries, like libc and libgcc. Since you supply your own crt0, add -nostartfiles to the arguments. So link with:
~/.programs/arm-gcc/bin/arm-none-eabi-gcc prog.o sysinit.o crt0.o uart.o \
-Wl,-Map=prog.map -Wl,-T../common/Teensy31_flash.ld -nostartfiles -o prog.elf