It appears that with gcc, it is only possible to compile programs using Intel's Math Kernel Library in 32 bit mode, as per installation instructions
source /opt/intel/mkl/bin/mklvars.sh ia32
gcc -m32 example_program.c -lmkl_intel -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm
If I try, for example
# Only options are ia32 or intel64
source /opt/intel/mkl/bin/mklvars.sh intel64
gcc example_program.c -lmkl_intel -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm
I get the error:
/usr/bin/ld: cannot find -lmkl_intel
Is it impossible to compile programs using the Math Kernel Library in 64 bit without using icc, Intel's own C compiler?
Edit: additionally, when compiling I get the message
/usr/bin/ld: skipping incompatible /opt/intel/compilers_and_libraries_2018.2.199/linux/mkl/lib/ia32_lin/libmkl_intel.so when searching for -lmkl_intel
/usr/bin/ld: skipping incompatible /opt/intel/compilers_and_libraries_2018.2.199/linux/mkl/lib/ia32_lin/libmkl_intel.a when searching for -lmkl_intel
When compiling with:
gcc hertzian_analysis_nd.c -L"/opt/intel/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64_lin/libmkl_intel_ilp64.a" -lmkl_intel -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm
I still get the same error.
Related
I'm trying to compile and link some .c file. I have been using Eclipse IDE for C/C++ developers, and in my local machine i can compile without problems. However, when i try to compile and link the same file in a RedHat OS (gcc version is 4.9.2-6 in this OS) i'm having problems. I get some warnings at compile time, but those are fine, i think, i just ignored and the application still runs fine. Here are the commands i executed and the associated output:
gcc -O0 -g3 -Wall -c -fmessage-length=0 -std=c99 -MMD -MP -MF"example.d" -MT"example.d" -o "example.o" "example.c"
warning: suggest parentheses around assignment used as truth value [-Wparentheses]
warning: implicit declaration of function ‘wait’ [-Wimplicit-function-declaration]
This generates two files, example.d and example.o. Then, i try to link them, without luck, with the following command:
gcc -Xlinker -L/usr/lib -lrt -static -pthread example.o -o example
/usr/bin/ld: cannot find -lrt
/usr/bin/ld: cannot find -lpthread
/usr/bin/ld: cannot find -lc
collect2: error: ld returned 1 exit status
The commands are taken directly from the ones that Eclipse generates, and work just fine in my local computer (Ubuntu OS) but not in the RedHat environment. The last command didn't work, with and without the -L option. I suppose the directory in -L is fine, as i run, for example,
locate libpthread.so
And one of the locations i get is /usr/lib (also /usr/lib64, but neither work).
Any help will be greatly appreciated!! :)
If you try to link a static executable, it will look for the *.a versions of the libraries, not what you usually want. Remove the -static flag. Or you can install the static libraries if you really want to. It also should not be necessary to add -L/usr/lib explicitly.
I am running mkl_lab_solution.c which is an example for using MKL, I can compile it correctly, while I run it, I got Segmentation fault.My runtime is below:
OS is centos 6.3
gcc's version is 4.1.2
mkl is mkl_10.3.12.361
makefile is below
gcc -g -L/opt/intel/composer_xe_2011_sp1.12.361/mkl/lib/intel64 -lmkl_intel_ilp64 -lmkl_intel_lp64 -lmkl_intel_sp2dp -lmkl_intel_thread -lmkl_core -lpthread -L/opt/intel/composer_xe_2011_sp1.12.361/compiler/lib/intel64 -liomp5 -L/usr/lib64 -lstdc++ -I/opt/intel/composer_xe_2011_sp1.12.361/mkl/include -o test mkl-lab-solution.c
Since this works fine on my system, let me point you to possible errors.
First, you need to run . /path/to/intel/compilervars.sh intel64 such all environment variables are set, like MKLROOT.
Second, check on intel mkl link line advisor for the options on your system. So reading your compile command I guess: linux, gnu compiler, dynamic linked, 64 bit target architecture, 64 bit long pointer, multithreaded, intel omp library.
These settings give me:
linker options:
-L$(MKLROOT)/lib/intel64 -lmkl_intel_ilp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm
compile options:
-DMKL_ILP64 -m64 -I$(MKLROOT)/include
For whatever reason the brackets around MKLROOT don't work on bash, so just remove them.
Next remember to put all compile options in front of linker options. The final command line should read like this:
gcc mkl-lab-solution.c -DMKL_ILP64 -m64 -I$MKLROOT/include -L$MKLROOT/lib/intel64 -lmkl_intel_ilp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm
Since you get runtime errors, I suspect that you are linking the Intel MKL libraries with objects compiled for different interface layers.
My program links to both PETSc and gsl, and both libraries were compiled with icc. Here's the link command:
/usr/local/mpich2/bin/mpicc -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g3 -I/usr/local/gsl-icc-1.15/include/ -I/usr/local/gsl-icc-1.15/include/ -L/usr/local/gsl-icc-1.15/lib/ -lgsl -lgslcblas prog_name.o -L/usr/local/petsc-3.2-p6/lib -lpetsc -lX11 -lpthread -llapack -lblas -L/central/intel/Compiler-11.1.072/mkl/lib/em64t -L/central/intel/Compiler-11.1.072/lib/intel64 -L/central/intel/Compiler-11.1.072/tbb/intel64/cc3.4.3_libc2.3.4_kernel2.6.9/lib -L/usr/lib/gcc/x86_64-redhat-linux/4.1.2 -ldl -lgcc_s -lifport -lifcore -limf -lsvml -lm -lipgo -lirc -lpthread -lirc_s -lm -lstdc++ -lstdc++ -ldl -lgcc_s -ldl -o prog_name
MPICH_CC is set to icc, so mpicc calls the intel compiler.
When I try to link to the gsl .so file, I get the following errors:
gsl-icc-1.15/lib/libgsl.so: undefined reference to `__intel_sse2_strcpy'
gsl-icc-1.15/lib/libgsl.so: undefined reference to `__intel_sse2_strchr'
gsl-icc-1.15/lib/libgsl.so: undefined reference to `__intel_sse2_strncpy'
What could be the cause of this error? Is gsl incompatible with the intel compiler?
What could be the cause of this error?
You didn't show us your link command, but my crystall ball tells me that you are trying to link libgsl.so with ld (or perhaps with gcc), instead of icc.
In general, one should never link anything directly with ld on UNIX. Always use appropriate compiler driver (icc in this case).
I also get the same error message when linking some code with gcc against a PETSc version that was compiled with icc. Even more, when using the newest Intel 12.x compiler for the final code, and compiling PETSc with Intel 11.x results in the same error message as Intel 12.x uses 11.x.
So check, that mpicc really use the Intel 11.1.072 compiler. Check for mpic++ -show and which icc.
Maybe the intel environment not set.
Try the following environment setting:
source /etc/Intel_Compiler/10.0/XXXX/iccvars_intel64.sh
source /etc/Intel_Compiler/10.0/XXXX/ifortvars_intel64.sh
make the folder to your Intel Compiler folder. Some version's environment setting is different, you can also try:
source /etc/Intel_Compiler/10.0/XXXX/iccvars.sh intel64
source /etc/Intel_Compiler/10.0/XXXX/ifortvars.sh intel64
Hope helpfully.
So I'm working through an assignment for Stanford's CS107 course and I can't get past compiling the unfinished program (project files and the original makefile can be found on the course page, I'm working on assignment 4 RSS.)
After much research, I think the problem is I'm using gcc on a 64-bit architecture (Mac OS 10.6) and the pre-compiled library code under assn-4-rss-news-search-lib/linux is for a 32-bit architecture. I tried setting gcc to use i386 and -m36, but nothings working and I'm kind of just guessing.
So here's the output I get when I run make:
gcc -g -Wall -std=gnu99 -Wno-unused-function -c -o rss-news-search.o rss-news-search.c
gcc rss-news-search.o -g -Wall -std=gnu99 -Wno-unused-function -g -lnsl -lrssnews -L/Users/derp/Documents/OCW/CS107/Work/programming4/assn-4-rss-news-search-lib/linux -o rss-news-search
ld: library not found for -lnsl
collect2: ld returned 1 exit status
make: *** [rss-news-search] Error 1
Here's the output I get when I remove -lnsl where architecture differences are mentioned:
gcc -g -Wall -std=gnu99 -Wno-unused-function -c -o rss-news-search.o rss-news-search.c
gcc rss-news-search.o -g -Wall -std=gnu99 -Wno-unused-function -g -lrssnews -L/Users/derp/Documents/OCW/CS107/Work/programming4/assn-4-rss-news-search-lib/linux -o rss-news-search
ld: warning: in /Users/derp/Documents/OCW/CS107/Work/programming4/assn-4-rss-news-search-lib/linux/librssnews.a, file was built for unsupported file format which is not the architecture being linked (x86_64)
Undefined symbols:
"_URLConnectionDispose", referenced from:
_ProcessFeed in rss-news-search.o
_ParseArticle in rss-news-search.o
... several more undefined symbols mentioned ...
ld: symbol(s) not found
collect2: ld returned 1 exit status
make: *** [rss-news-search] Error 1
So I'm asking for any ideas on what I could do to resolve this. I've been at it for hours tweaking settings and Google'ing around to no avail.
In case someone like me will be looking for answer after all this time passed...
Problem is easy solved by installing wubi version of 32bit Ubuntu. It works fine on 64bit system. You only need to edit makefile so it knows where to look for the libraries provided.
I'm pretty sure that using a precompiled library for linux on macos, whatever the bitness, won't work (well, it is probably possible to cross-compile on MacOS for Linux and perhaps possible to run Linux executable in a compatibility box on MacOS, but that's quite different than what you are trying to do).
libnsl is a standard library on Linux (it provides some networking related functions)
I'm trying to use someone else's Makefile to complile a very simple c++ library. The makefile is as follows:
JNIFLAGS=-O2 -pthread -I/usr/lib/jvm/java-6-sun/include -I/usr/lib/jvm/java-6-sun/include/linux
all:
rm -f ../dist/libUtils.so
g++ $(JNIFLAGS) -c -m32 -o com_markets_utils_dates_NativeTime.o com_markets_utils_dates_NativeTime.cpp
g++ $(JNIFLAGS) -c -m32 -o DateUtil.o DateUtil.cpp
g++ -pthread -m32 -shared -fPIC -o ../dist/libUtils.so DateUtil.cpp
g++ -pthread -m32 -shared -fPIC -o ../dist/libNativeTime.so DateUtil.o com_markets_utils_dates_NativeTime.o
This compiles fine, but the linker complains:
...
/usr/bin/ld: skipping incompatible /usr/lib/gcc/x86_64-linux-gnu/4.4.1/libstdc++.so when searching for -lstdc++
/usr/bin/ld: skipping incompatible /usr/lib/gcc/x86_64-linux-gnu/4.4.1/libstdc++.a when searching for -lstdc++
/usr/bin/ld: skipping incompatible /usr/lib/gcc/x86_64-linux-gnu/4.4.1/libstdc++.so when searching for -lstdc++
/usr/bin/ld: skipping incompatible /usr/lib/gcc/x86_64-linux-gnu/4.4.1/libstdc++.a when searching for -lstdc++
/usr/bin/ld: cannot find -lstdc++
collect2: ld returned 1 exit status
make: *** [all] Error 1
FYI, I am on Ubuntu 9.10 64bit.
Posting for future reference, a solution I found was to install g++-multilib. I had the same incompatible problem relating to -lstdc++ on g++ version 4.6.1
On further probing: g++-multilib is a dummy package which installed g++4.6-multilib which in turn installed the appropriate libstdc++.so under the /usr/lib/gcc/x86_64-linux-gnu/4.6/32 folder.
Answering my own question:
Ths solution seems to be a bit of a hack, you need to create a symlink for the 32 bit version of the library (after installing the packages mentioned in #nos's answer):
$ sudo ln -s /usr/lib32/libstdc++.so.6 /usr/lib32/libstdc++.so
Once you've done this, the linker will automagically find the correct library to use.
It seems you're compiling a 32 bit library on a 64 bit machine, however a 32 bit version of libstdc++ is not present.
Try apt-get install ia32-libs libc6-i386 libc6-dev-i386 lib32gcc1 lib32stdc++6
(btw. you're producing a .so , you should specify -fPIC when compiling your .cpp files as well)