[Q-e-developers] [Pw_forum] QE-GPU: compilation error with Espresso 5.1

Mauro Sgroi maurofrancesco.sgroi at gmail.com
Mon Sep 8 10:47:42 CEST 2014 

Dear Filippo,
I'm using now gcc 4.4 wih the internal blas/lapack libraries, just to
reduce the complexity of the problem.
I modified GPU/install/make_phiGEMM.inc to link with -lgfortran to solve
some undefined reference errors.
But now the compilation stops with an undefined reference to `main'.
Thanks a lot and best regards,
Mauro.


Make[3]: Entering directory `/usr/local/src/espresso-5.1_gpu/phiGEMM/src'
mkdir -p ../bin ../lib
ar ruv libphigemm.a phigemm_auxiliary.o phigemm_env.o phigemm_dgemm.o
phigemm_zgemm.o phigemm_dgemm_specialK.o phigemm_zgemm_specialK.o
phigemm_cgemm.o phigemm_sgemm.o
ar: creating libphigemm.a
a - phigemm_auxiliary.o
a - phigemm_env.o
a - phigemm_dgemm.o
a - phigemm_zgemm.o
a - phigemm_dgemm_specialK.o
a - phigemm_zgemm_specialK.o
a - phigemm_cgemm.o
a - phigemm_sgemm.o
mv libphigemm.a ../lib/.
mkdir -p ../bin ../lib
gcc -O3 -fopenmp -fPIC -z muldefs -lgfortran  -o libphigemm.so.2.0
phigemm_auxiliary.o phigemm_env.o phigemm_dgemm.o phigemm_zgemm.o
phigemm_dgemm_specialK.o phigemm_zgemm_specialK.o phigemm_cgemm.o
phigemm_sgemm.o -L/usr/local/cuda-6.0/lib64 -lcublas  -lcufft -lcudart
/usr/local/src/espresso-5.1_gpu/GPU/..//phiGEMM/lib/libphigemm.a
 /usr/local/src/espresso-5.1_gpu/GPU/..//BLAS/blas.a
-L/usr/local/cuda-6.0/lib64 -lcublas  -lcufft -lcudart -lgfortran
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../lib64/crt1.o: In
function `_start':
(.text+0x20): undefined reference to `main'
collect2: ld returned 1 exit status
make[3]: *** [shared] Error 1
make[3]: Leaving directory `/usr/local/src/espresso-5.1_gpu/phiGEMM/src'
make[2]: *** [phigemm] Error 2
make[2]: Leaving directory `/usr/local/src/espresso-5.1_gpu/phiGEMM'
make[1]: *** [libphiGEMM] Error 2
make[1]: Leaving directory `/usr/local/src/espresso-5.1_gpu/GPU/install'
make: *** [libphiGEMM] Error 2


2014-09-06 10:43 GMT+02:00 Filippo Spiga <spiga.filippo at gmail.com>:

> Dear Mauro,
>
> I understand you want to use OpenBLAS based on how you tried to run the
> configure the first time. After configure, before make, change both
> make.sys and GPU/install/make_phiGEMM.inc  to point to Open BLAS
>
> What version of GCC are you using? My suggestion is 4.4 or 4.6. You can
> also download Intel MKL runtime library from Intel website and link them
> with GCC to QE and QE-GPU. Performance will be better than internal
> BLAS/LAPACK and the configure pick the libraries up automatically (not like
> OpenBLAS)
>
> HTH
> F
>
>
> > On Sep 5, 2014, at 2:59 PM, Mauro Sgroi <maurofrancesco.sgroi at gmail.com>
> wrote:
> >
> > Dear Filippo,
> > I created a brand new directory of QE just for the GPU compilation and
> I'm trying now to use the configure command indicated in the README.
> > The error now is the following, it seems that phiGEMM doesn't find
> libgfortran.
> >
> > make[3]: Entering directory `/usr/local/src/espresso-5.1_gpu/phiGEMM/src'
> > /usr/local/cuda-6.0/bin/nvcc -ccbin gcc -O3 --compiler-options '-c -fPIC
> -fopenmp' -D__PHIGEMM_WEAK_INTERFACES -D__PHIGEMM_SELFTUNE
> -D__PHIGEMM_ENABLE_SPECIALK
> -I/usr/local/src/espresso-5.1_gpu/GPU/..//phiGEMM/include
> -I/usr/local/cuda-6.0/include -I../include/ -c phigemm_auxiliary.c -o
> phigemm_auxiliary.o
> > nvcc warning : The 'compute_10' and 'sm_10' architectures are
> deprecated, and may be removed in a future release.
> > /usr/local/cuda-6.0/bin/nvcc -ccbin gcc -O3 --compiler-options '-c -fPIC
> -fopenmp' -D__PHIGEMM_WEAK_INTERFACES -D__PHIGEMM_SELFTUNE
> -D__PHIGEMM_ENABLE_SPECIALK
> -I/usr/local/src/espresso-5.1_gpu/GPU/..//phiGEMM/include
> -I/usr/local/cuda-6.0/include -I../include/ -c phigemm_env.c -o
> phigemm_env.o
> > nvcc warning : The 'compute_10' and 'sm_10' architectures are
> deprecated, and may be removed in a future release.
> > /usr/local/cuda-6.0/bin/nvcc -ccbin gcc -O3 --compiler-options '-c -fPIC
> -fopenmp' -D__PHIGEMM_WEAK_INTERFACES -D__PHIGEMM_SELFTUNE
> -D__PHIGEMM_ENABLE_SPECIALK
> -I/usr/local/src/espresso-5.1_gpu/GPU/..//phiGEMM/include
> -I/usr/local/cuda-6.0/include -I../include/ -c phigemm_dgemm.c -o
> phigemm_dgemm.o
> > nvcc warning : The 'compute_10' and 'sm_10' architectures are
> deprecated, and may be removed in a future release.
> > /usr/local/cuda-6.0/bin/nvcc -ccbin gcc -O3 --compiler-options '-c -fPIC
> -fopenmp' -D__PHIGEMM_WEAK_INTERFACES -D__PHIGEMM_SELFTUNE
> -D__PHIGEMM_ENABLE_SPECIALK
> -I/usr/local/src/espresso-5.1_gpu/GPU/..//phiGEMM/include
> -I/usr/local/cuda-6.0/include -I../include/ -c phigemm_zgemm.c -o
> phigemm_zgemm.o
> > nvcc warning : The 'compute_10' and 'sm_10' architectures are
> deprecated, and may be removed in a future release.
> > /usr/local/cuda-6.0/bin/nvcc -ccbin gcc -O3 --compiler-options '-c -fPIC
> -fopenmp' -D__PHIGEMM_WEAK_INTERFACES -D__PHIGEMM_SELFTUNE
> -D__PHIGEMM_ENABLE_SPECIALK
> -I/usr/local/src/espresso-5.1_gpu/GPU/..//phiGEMM/include
> -I/usr/local/cuda-6.0/include -I../include/ -c phigemm_dgemm_specialK.c -o
> phigemm_dgemm_specialK.o
> > nvcc warning : The 'compute_10' and 'sm_10' architectures are
> deprecated, and may be removed in a future release.
> > /usr/local/cuda-6.0/bin/nvcc -ccbin gcc -O3 --compiler-options '-c -fPIC
> -fopenmp' -D__PHIGEMM_WEAK_INTERFACES -D__PHIGEMM_SELFTUNE
> -D__PHIGEMM_ENABLE_SPECIALK
> -I/usr/local/src/espresso-5.1_gpu/GPU/..//phiGEMM/include
> -I/usr/local/cuda-6.0/include -I../include/ -c phigemm_zgemm_specialK.c -o
> phigemm_zgemm_specialK.o
> > nvcc warning : The 'compute_10' and 'sm_10' architectures are
> deprecated, and may be removed in a future release.
> > /usr/local/cuda-6.0/bin/nvcc -ccbin gcc -O3 --compiler-options '-c -fPIC
> -fopenmp' -D__PHIGEMM_WEAK_INTERFACES -D__PHIGEMM_SELFTUNE
> -D__PHIGEMM_ENABLE_SPECIALK
> -I/usr/local/src/espresso-5.1_gpu/GPU/..//phiGEMM/include
> -I/usr/local/cuda-6.0/include -I../include/ -c phigemm_cgemm.c -o
> phigemm_cgemm.o
> > nvcc warning : The 'compute_10' and 'sm_10' architectures are
> deprecated, and may be removed in a future release.
> > /usr/local/cuda-6.0/bin/nvcc -ccbin gcc -O3 --compiler-options '-c -fPIC
> -fopenmp' -D__PHIGEMM_WEAK_INTERFACES -D__PHIGEMM_SELFTUNE
> -D__PHIGEMM_ENABLE_SPECIALK
> -I/usr/local/src/espresso-5.1_gpu/GPU/..//phiGEMM/include
> -I/usr/local/cuda-6.0/include -I../include/ -c phigemm_sgemm.c -o
> phigemm_sgemm.o
> > nvcc warning : The 'compute_10' and 'sm_10' architectures are
> deprecated, and may be removed in a future release.
> > mkdir -p ../bin ../lib
> > ar ruv libphigemm.a phigemm_auxiliary.o phigemm_env.o phigemm_dgemm.o
> phigemm_zgemm.o phigemm_dgemm_specialK.o phigemm_zgemm_specialK.o
> phigemm_cgemm.o phigemm_sgemm.o
> > ar: creating libphigemm.a
> > a - phigemm_auxiliary.o
> > a - phigemm_env.o
> > a - phigemm_dgemm.o
> > a - phigemm_zgemm.o
> > a - phigemm_dgemm_specialK.o
> > a - phigemm_zgemm_specialK.o
> > a - phigemm_cgemm.o
> > a - phigemm_sgemm.o
> > mv libphigemm.a ../lib/.
> > mkdir -p ../bin ../lib
> > cc -O3 -fopenmp -fPIC -z muldefs  -o libphigemm.so.2.0
> phigemm_auxiliary.o phigemm_env.o phigemm_dgemm.o phigemm_zgemm.o
> phigemm_dgemm_specialK.o phigemm_zgemm_specialK.o phigemm_cgemm.o
> phigemm_sgemm.o -L/usr/local/cuda-6.0/lib64 -lcublas  -lcufft -lcudart
> /usr/local/src/espresso-5.1_gpu/GPU/..//phiGEMM/lib/libphigemm.a
> /usr/local/src/espresso-5.1_gpu/GPU/..//BLAS/blas.a
> -L/usr/local/cuda-6.0/lib64 -lcublas  -lcufft -lcudart
> > /usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../lib64/crt1.o: In
> function `_start':
> > (.text+0x20): undefined reference to `main'
> > /usr/local/src/espresso-5.1_gpu/GPU/..//BLAS/blas.a(xerbla.o): In
> function `xerbla_':
> > xerbla.f:(.text+0x51): undefined reference to `_gfortran_st_write'
> > xerbla.f:(.text+0x61): undefined reference to
> `_gfortran_transfer_character'
> > xerbla.f:(.text+0x71): undefined reference to
> `_gfortran_transfer_integer'
> > xerbla.f:(.text+0x79): undefined reference to `_gfortran_st_write_done'
> > xerbla.f:(.text+0x83): undefined reference to `_gfortran_stop_numeric'
> > collect2: ld returned 1 exit status
> > make[3]: *** [shared] Error 1
> > make[3]: Leaving directory `/usr/local/src/espresso-5.1_gpu/phiGEMM/src'
> > make[2]: *** [phigemm] Error 2
> > make[2]: Leaving directory `/usr/local/src/espresso-5.1_gpu/phiGEMM'
> > make[1]: *** [libphiGEMM] Error 2
> > make[1]: Leaving directory `/usr/local/src/espresso-5.1_gpu/GPU/install'
> >
> >
> > Moreover I have some more questions about the integration of external
> BLAS, LAPACK and FFTW libraries.
> > Is it useful in terms of speed to insert manually openblas and fftw3 in
> the make.sys?
> > Moreover, having a single PC with a 8-cores processor and a single GPU,
> it does make sense to compile the parallel version? Or it's better to use
> the seria/OMP version? In this last case, how many threads should I use?
> >
> > Sorry for the multiple (probably silly) questions..
> > Best regards,
> > Mauro Sgroi
> > Centro Ricerche FIAT
> > Italia
> >
> >
> >
> >
> > 2014-09-05 9:47 GMT+02:00 Filippo Spiga <spiga.filippo at gmail.com>:
> > Dear Mauro,
> >
> > After configure, what is the text after DFLAGS = inside make.sys?
> >
> > I suspect two things:
> > - it looks like there are dirty object files around, please  "make -f
> Makefile.gpu distclean" first
> > - by override FFT_LIBS, BLAS_LIBS and LAPACK_LIBS some of the internal
> checkings in the configure do not work properly
> >
> > My strong suggestion is to edit make.sys after you run the configure,
> overriding FFT_LIBS, BLAS_LIBS and LAPACK_LIBS only if it is strictly
> necessary. In your particular case, by doing so you miss phiGEMM and MAGMA
> and other libraries to link to the final executable. I am improving over
> time the configure but it will take time to percolate these changes to the
> main distribution and into QE-GPU. I can add OpenBLAS support to the
> configure natively, it is not a process that take one day.
> >
> > Speaking about CUDA 6.5, I has trouble running MAGMA with the latest
> CUDA toolkit recently. So my suggestion is to use a more stable CUDA 6.0 or
> temporary disable MAGMA. It is worh try but if the application has problems
> this is the first thing to remove.
> >
> > HTH
> > F
> >
> >
> > On Sep 4, 2014, at 3:37 PM, Mauro Sgroi <maurofrancesco.sgroi at gmail.com>
> wrote:
> > > Dear Developers.
> > > I'm trying to install the GPU version of Quantum Espresso 5.1.
> > > I'm using RedHat EL 6.3 with the gcc 4.4.6 compiler and Cuda Toolkit
> 6.5.
> > > My configure command is as follows:
> > >
> > > configure FFT_LIBS='-L/usr/local/lib/ -lfftw3'
> LAPACK_LIBS='-L/usr/local/lib -lopenblas' --disable-parallel
> --enable-openmp --enable-cuda --with-gpu-arch=sm_30
> --with-cuda-dir=/usr/local/cuda --with-magma --with-phigemm
> BLAS_LIBS='-L/usr/local/lib -lopenblas'
> > >
> > > and I get the following error:
> > >
> > > make[1]: Entering directory
> `/usr/local/src/espresso-5.1_GPU/GPU/Modules'
> > > ( if test -x ../install/update_gpu_version ; then \
> > >         ../install/update_gpu_version; \
> > >         else if test ! -f ../include/gpu-version.h ; then \
> > >         cat ../include/gpu-version.h.in > ../include/gpu-version.h ;
> fi ; fi )
> > > nvcc -ccbin=/usr/bin  -I../../include -I../include -D__GFORTRAN
> -D__STD_F95 -D__FFTW -D__OPENMP    -c cuda_init.cu
> > > cuda_init.cu(361): error: identifier "ngpus_per_process" is undefined
> > >
> > > cuda_init.cu(363): error: identifier "qe_gpu_bonded" is undefined
> > >
> > > cuda_init.cu(376): error: identifier "qe_gpu_kernel_launch" is
> undefined
> > >
> > > cuda_init.cu(376): error: identifier "update_gpu_kernel_specs" is
> undefined
> > >
> > > cuda_init.cu(413): warning: variable "lRankThisNode" was declared but
> never referenced
> > >
> > > cuda_init.cu(413): warning: variable "lSizeThisNode" was declared but
> never referenced
> > >
> > > 4 errors detected in the compilation of
> "/tmp/tmpxft_00004217_00000000-6_cuda_init.cpp1.ii".
> > > make[1]: *** [cuda_init.o] Error 2
> > > make[1]: Leaving directory
> `/usr/local/src/espresso-5.1_GPU/GPU/Modules'
> > > make: *** [gpu-mods] Error 2
> > >
> > >
> > > Could you help me with this problem?
> > > Thanks a lot in advance and best regards,
> > > Mauro Sgroi.
> > > _______________________________________________
> > > Pw_forum mailing list
> > > Pw_forum at pwscf.org
> > > http://pwscf.org/mailman/listinfo/pw_forum
> >
> > --
> > Mr. Filippo SPIGA, M.Sc.
> > http://filippospiga.info ~ skype: filippo.spiga
> >
> > «Nobody will drive us out of Cantor's paradise.» ~ David Hilbert
> >
> > *****
> > Disclaimer: "Please note this message and any attachments are
> CONFIDENTIAL and may be privileged or otherwise protected from disclosure.
> The contents are not to be disclosed to anyone other than the addressee.
> Unauthorized recipients are requested to preserve this confidentiality and
> to advise the sender immediately of any error in transmission."
> >
> >
> >
> > _______________________________________________
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> > Pw_forum at pwscf.org
> > http://pwscf.org/mailman/listinfo/pw_forum
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://pwscf.org/mailman/listinfo/pw_forum
>
> --
> Mr. Filippo SPIGA, M.Sc.
> http://filippospiga.info ~ skype: filippo.spiga
>
> «Nobody will drive us out of Cantor's paradise.» ~ David Hilbert
>
> *****
> Disclaimer: "Please note this message and any attachments are CONFIDENTIAL
> and may be privileged or otherwise protected from disclosure. The contents
> are not to be disclosed to anyone other than the addressee. Unauthorized
> recipients are requested to preserve this confidentiality and to advise the
> sender immediately of any error in transmission."
>
>
>
> _______________________________________________
> Pw_forum mailing list
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