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

[Mauro Sgroi]

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
>
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