topic Before I run make, I run the in Software Archive

Linking C++ and Fortran objects

Georgi_G_1 — Tue, 06 Oct 2015 13:32:11 GMT

Platform: CentOS release 6.6 (Final)

GCC: 4.9.1

Intel Parallel Studio Cluster Edition 2016

I am working on a bioinformatics application that my team and I have successfully compiled for Intel Xeon processor. Now we're trying to compile the application for MIC but we have a hard time linking it. The error that we get is the following:

x86_64-k1om-linux-ld: cannot find -lstadc++
/opt/mpss/3.2.1/sysroots/x86_64-mpsssdk-linux/lib/libc-2.14.90.so: could not read symbols: File in wrong format

I have attached the makefile. Also, is there a tutorial on how to link multiple languages together for MIC because I was searching for a long time and couldn't find anything useful.

Is sta++ a misspelling of std

TimP — Tue, 06 Oct 2015 14:02:49 GMT

Is sta++ a misspelling of std++ ? You must use -mmic consistently for both compile and link, debug or no debug. When you try to link k1om Mic objects against host libraries you will see such link errors.

The sta++ was a type, I

Georgi_G_1 — Tue, 06 Oct 2015 14:18:00 GMT

The sta++ was a typo, I corrected it. I also changed the makefile but the error about the wrong format persists. I attach the updated makefile

Nobody has an idea how to

Georgi_G_1 — Fri, 09 Oct 2015 01:30:35 GMT

Nobody has an idea how to solve this problem?

My apologies. I should have

Frances_R_Intel — Fri, 09 Oct 2015 02:33:00 GMT

My apologies. I should have gotten to this earlier.

Prior to using the Intel compilers, you should execute "source {installation_dir}/parallel_studio_xe_{version}/bin/psxevars.sh intel64" (or ". {installation_dir}/parallel_studio_xe_{version}/bin/psxevars.csh intel64" for csh). From your make file it looks like installation_dir is /srv/michome/gdg217/intel/. It is difficult to set the library paths yourself. From your makefile, it appears there are a number of files missing. I believe you should be able to prepend the path to those debug libraries after that but make sure you prepend the mic path to MIC_LD_LIBRARY_PATH. See if that helps.

Before I run make, I run the

Georgi_G_1 — Fri, 09 Oct 2015 03:29:29 GMT

Before I run make, I run the following commands:

source compilevars.sh intel64

source iccvars.sh intel64

source ifortvars.sh intel64

source ~/intel/parallel_studio_2016/bin/psxvars.sh intel64

export MIC_LD_LIBRARY_PATH=/home/gdg217/intel/lib/mic/

make

Result - still the same error:

/opt/mpss/3.2.1/sysroots/x86_64-mpsssdk-linux/lib/libc-2.14.90.so: could not read symbols: File in wrong format

----------------

file /opt/mpss/3.2.1/sysroots/x86_64-mpsssdk-linux/lib/libc-2.14.90.so

-> /opt/mpss/3.2.1/sysroots/x86_64-mpsssdk-linux/lib/libc-2.14.90.so: ELF 64-bit LSB shared object, x86-64, version 1 (SYSV), dynamically linked (uses shared libs), for GNU/Linux 2.6.16, stripped

Right, I just realized I

Frances_R_Intel — Fri, 09 Oct 2015 11:09:32 GMT

Right, I just realized I messed up. Of course you have sourced that file. If you hadn't, your makefile would have blown up.

Let's see if I can get it right this time.

You only need "source ~/intel/parallel_studio_2016/bin/psxvars.sh intel64". That script runs {install_dir}/compilers_and_libraries_{version}/linux/bin/compilervars.sh. The files iccvars.sh and ifortvars.sh are now aliases for compilervars.sh. Once you have run psxvars.sh, do not write over MIC_LD_LIBRARY_PATH or MIC_LIBRARY_PATH. If you have local libraries (which I don't see), you can append their location to MIC_LD_LIBRARY_PATH or MIC_LIBRARY_PATH as appropriate but don't write over them.

After that I would let the icc and ifort figure out which libraries they need based on the flags you set rather than trying to find the right ones yourself.

To use the debug libraries for tbb, add -DTBB_USE_DEBUG to your flags. You should not need to explicitly specify the names or locations of the debug libraries when MIC_LD_LIBRARY_PATH is set correctly. So I think you should comment out those lines.

I'm not sure why you are specifying /opt/mpss/3.2.1/sysroots/x86_64-mpsssdk-linux/lib/libc-2.14.90.so and {install_dir}/advisor_xe_2016.1.0.423501/lib64/pinruntime/glibc/libc.so.6 in LIBS. They will conflict. Again, I think you should comment that out and let the compiler find the right library.

Finally, I don't think it is a good idea to specify --dynamic-linker. Let icc and ifort choose the right one.

I followed your advice and

Georgi_G_1 — Sat, 10 Oct 2015 19:29:00 GMT

Thank you!!!

I followed your advice and changed the makefile. I tried again and I got a few pages of errors of undefined references before realizing that I had to put the library links (-ltbb) after the -o flag. I fixed that error and it worked perfectly. I attach the makefile for other people's reference.

Note: I also had to export the path to libtbb.so.2 because I didn't have root access to the machine and the installation is local

[SOLVED]