Error while using -static and -L/usr/lib/x86_64-redhat-linux5E/lib64/ on Linux x64 platform

lee_icc · ‎06-16-2013

Dear All,

I tried to compile my C code using Eclipse with Intel C/C++ compiler 13.1.1 on scientific linux 6.4 x64 platform. When linked dynamically, it was successful with no error or warnings. When linked with -static and -L/usr/lib/x86_64-redhat-linux5E/lib64/, it reported many error about undefined reference shown as follows:

make -k all
Building file: ../src/mcmc_demo.c
Invoking: Intel Intel(R) 64 C Compiler
icc -O3 -ip -mkl=parallel -openmp -MMD -MP -MF"src/mcmc_demo.d" -MT"src/mcmc_demo.d" -c -o "src/mcmc_demo.o" "../src/mcmc_demo.c"
Finished building: ../src/mcmc_demo.c

Building target: mcmc_demo
Invoking: Intel Intel(R) 64 C Linker
icc -static -openmp -mkl=parallel -O3 -L/usr/lib/x86_64-redhat-linux5E/lib64/ -o "mcmc_demo" ./src/mcmc_demo.o
./src/mcmc_demo.o: In function `main':
../src/mcmc_demo.c:(.text+0x71): undefined reference to `__isoc99_fscanf'
../src/mcmc_demo.c:(.text+0x100): undefined reference to `__isoc99_fscanf'
../src/mcmc_demo.c:(.text+0x174): undefined reference to `__isoc99_fscanf'
../src/mcmc_demo.c:(.text+0x230): undefined reference to `__isoc99_fscanf'
../src/mcmc_demo.c:(.text+0x43a): undefined reference to `__isoc99_fscanf'
../src/mcmc_demo.c:(.text+0x5ed): undefined reference to `vdLn'
../src/mcmc_demo.c:(.text+0xd00): undefined reference to `vslNewStream'
../src/mcmc_demo.c:(.text+0xd28): undefined reference to `vdRngUniform'
../src/mcmc_demo.c:(.text+0xd42): undefined reference to `vdLn'
../src/mcmc_demo.c:(.text+0xe15): undefined reference to `vdRngGaussian'
../src/mcmc_demo.c:(.text+0xeac): undefined reference to `vdLn'
../src/mcmc_demo.c:(.text+0x1561): undefined reference to `cblas_dcopy'
../src/mcmc_demo.c:(.text+0x159f): undefined reference to `cblas_dcopy'
../src/mcmc_demo.c:(.text+0x1607): undefined reference to `cblas_dcopy'
../src/mcmc_demo.c:(.text+0x1645): undefined reference to `cblas_dcopy'
../src/mcmc_demo.c:(.text+0x16b1): undefined reference to `cblas_dcopy'
../src/mcmc_demo.c:(.text+0x175f): undefined reference to `vslDeleteStream'
./src/mcmc_demo.o: In function `asm2d':
../src/mcmc_demo.c:(.text+0x8184): undefined reference to `cblas_dgemv'
./src/mcmc_demo.o: In function `logpriorfun':
../src/mcmc_demo.c:(.text+0x81c3): undefined reference to `vdLn'
./src/mcmc_demo.o: In function `proprnd':
../src/mcmc_demo.c:(.text+0x8470): undefined reference to `vdRngGaussian'
make: *** [mcmc_demo] Error 1
make: Target `all' not remade because of errors.

Does anyone have idea that how to resolve this issue? Thanks in advance.

Lee

SergeyKostrov · ‎06-17-2013

>>... >>../src/mcmc_demo.c:(.text+0x5ed): undefined reference to `vdLn' >>../src/mcmc_demo.c:(.text+0xd00): undefined reference to `vslNewStream' >>../src/mcmc_demo.c:(.text+0xd28): undefined reference to `vdRngUniform' >>../src/mcmc_demo.c:(.text+0xd42): undefined reference to `vdLn' >>../src/mcmc_demo.c:(.text+0xe15): undefined reference to `vdRngGaussian' >>../src/mcmc_demo.c:(.text+0xeac): undefined reference to `vdLn' >>../src/mcmc_demo.c:(.text+0x1561): undefined reference to `cblas_dcopy' >>../src/mcmc_demo.c:(.text+0x159f): undefined reference to `cblas_dcopy' >>../src/mcmc_demo.c:(.text+0x1607): undefined reference to `cblas_dcopy' >>../src/mcmc_demo.c:(.text+0x1645): undefined reference to `cblas_dcopy' >>../src/mcmc_demo.c:(.text+0x16b1): undefined reference to `cblas_dcopy' >>../src/mcmc_demo.c:(.text+0x175f): undefined reference to `vslDeleteStream' >>... These are MKL functions and please verify that in that case a right path to MKL libraries is used.

lee_icc · ‎06-17-2013

Yes, the path to MKL libraries is correct. When linked dynamically (without -static or -static-intel option), it was OK with no error or warnings. These error were only reported while linking statically.

SergeyKostrov · ‎06-17-2013

>>...icc -static -openmp -mkl=parallel -O3 -L/usr/lib/x86_64-redhat-linux5E/lib64/ -o "mcmc_demo" ./src/mcmc_demo.o There is a difference between 1st command line and the 2nd ( I marked a path to some folder with 64-bit libraries ). Why don't you use that path in the 1st case? Or, why do you use the path in the 2nd case?

lee_icc · ‎06-17-2013

The log shown in my previous post was copied from the Eclipse console output. I also tested it in command line:

[sl@localhost test]$ icc -O3 -ip -mkl=parallel -openmp -static mcmc_demo.c
ld: cannot find -lm

Following the webpage http://software.intel.com/en-us/forums/topic/277227 and http://software.intel.com/en-us/articles/error-ld-cannot-find-lm/, I tested the new compile options:

[sl@localhost test]$ icc -O3 -ip -mkl=parallel -openmp -static mcmc_demo.c -L/usr/lib/x86_64-redhat-linux5E/lib64/
/tmp/iccondg4F.o: In function `main':
mcmc_demo.c:(.text+0x71): undefined reference to `__isoc99_fscanf'
mcmc_demo.c:(.text+0x100): undefined reference to `__isoc99_fscanf'
mcmc_demo.c:(.text+0x174): undefined reference to `__isoc99_fscanf'
mcmc_demo.c:(.text+0x230): undefined reference to `__isoc99_fscanf'
mcmc_demo.c:(.text+0x43a): undefined reference to `__isoc99_fscanf'
mcmc_demo.c:(.text+0x5ed): undefined reference to `vdLn'
mcmc_demo.c:(.text+0xd00): undefined reference to `vslNewStream'
mcmc_demo.c:(.text+0xd28): undefined reference to `vdRngUniform'
mcmc_demo.c:(.text+0xd42): undefined reference to `vdLn'
mcmc_demo.c:(.text+0xe15): undefined reference to `vdRngGaussian'
mcmc_demo.c:(.text+0xeac): undefined reference to `vdLn'
mcmc_demo.c:(.text+0x1561): undefined reference to `cblas_dcopy'
mcmc_demo.c:(.text+0x159f): undefined reference to `cblas_dcopy'
mcmc_demo.c:(.text+0x1607): undefined reference to `cblas_dcopy'
mcmc_demo.c:(.text+0x1645): undefined reference to `cblas_dcopy'
mcmc_demo.c:(.text+0x16b1): undefined reference to `cblas_dcopy'
mcmc_demo.c:(.text+0x175f): undefined reference to `vslDeleteStream'
/tmp/iccondg4F.o: In function `asm2d':
mcmc_demo.c:(.text+0x8184): undefined reference to `cblas_dgemv'
/tmp/iccondg4F.o: In function `logpriorfun':
mcmc_demo.c:(.text+0x81c3): undefined reference to `vdLn'
/tmp/iccondg4F.o: In function `proprnd':
mcmc_demo.c:(.text+0x8470): undefined reference to `vdRngGaussian'

When using 'icc -O3 -ip -mkl=parallel -openmp mcmc_demo.c', it works fine and built the executalbe 'a.out' without any error. It seem that the issue is related to the function 'fscanf' and static linking to MKL.

SergeyKostrov · ‎06-18-2013

>>...mcmc_demo.c:(.text+0x71): undefined reference to `__isoc99_fscanf' Could you try to enable support for C99 language standard?

lee_icc · ‎06-19-2013

Enabling C99 support with the option -std=c99 did not help to resolve the '__isoc99_fscanf' error:

[sl@localhost test]$ icc -O3 -ip -std=c99 -mkl=parallel -openmp -static mcmc_demo.c -L/usr/lib/x86_64-redhat-linux5E/lib64/
/tmp/icct1sV8V.o: In function `main':
mcmc_demo.c:(.text+0x71): undefined reference to `__isoc99_fscanf'
mcmc_demo.c:(.text+0x100): undefined reference to `__isoc99_fscanf'
mcmc_demo.c:(.text+0x174): undefined reference to `__isoc99_fscanf'
mcmc_demo.c:(.text+0x230): undefined reference to `__isoc99_fscanf'
mcmc_demo.c:(.text+0x43a): undefined reference to `__isoc99_fscanf'
mcmc_demo.c:(.text+0x5ed): undefined reference to `vdLn'
...

Following the advice by Ying (http://software.intel.com/en-us/comment/1740145#comment-1740145), explictly linking MKL resolved the error 'undefined reference' to MKL functions.

After several test, I also found that using the option '-L/usr/lib/x86_64-redhat-linux5E/lib64/' leads to undefined reference to `__isoc99_fscanf'. Without this option, it reported 'ld: cannot find -lpthread' instead. Detailed logs are as follows:

[sl@localhost test]$ icc -O3 -ip -openmp -static mcmc_demo.c -Wl,--start-group $MKLROOT/lib/intel64/libmkl_intel_lp64.a $MKLROOT/lib/intel64/libmkl_intel_thread.a $MKLROOT/lib/intel64/libmkl_core.a -Wl,--end-group -lpthread -lm
ld: cannot find -lpthread

[sl@localhost test]$ icc -O3 -ip -openmp -static mcmc_demo.c -L/usr/lib/x86_64-redhat-linux5E/lib64/ -Wl,--start-group $MKLROOT/lib/intel64/libmkl_intel_lp64.a $MKLROOT/lib/intel64/libmkl_intel_thread.a $MKLROOT/lib/intel64/libmkl_core.a -Wl,--end-group -lpthread -lm
/tmp/iccZTzhHD.o: In function `main':
mcmc_demo.c:(.text+0x71): undefined reference to `__isoc99_fscanf'
mcmc_demo.c:(.text+0x100): undefined reference to `__isoc99_fscanf'
mcmc_demo.c:(.text+0x174): undefined reference to `__isoc99_fscanf'
mcmc_demo.c:(.text+0x230): undefined reference to `__isoc99_fscanf'
mcmc_demo.c:(.text+0x43a): undefined reference to `__isoc99_fscanf'

SergeyKostrov · ‎06-19-2013

I see that there are two similar threads and another one is: Forum Topic: Error in static linking to MKL on Linux x64 platform Web-link: http://software.intel.com/en-us/forums/topic/393920

lee_icc · ‎06-19-2013

Yes, I also reported the issue to MKL forum to resolve the issue on static linking MKL. I am sorry for my duplicate posts. Thank you very much for your help, Sergey.