[Pw_forum] GPU14.03 compiling error

PePe pepe.physics at gmail.com
Tue Apr 8 03:55:43 CEST 2014 

I linked quark with the directory in qe-magma,

ln -s quark qe-magma/exp/quark

now when I compile with make -f Makefile.gpu pw-gpu LD_SHARED_FLAGS=-shared
I get an error

make[1]: Leaving directory `/home/pepe/src/espresso-5.0.99/PW/src'
if test -d GPU/PW ; then \
        ( cd GPU/PW ; if test "make" = "" ; then make  TLDEPS= all ; \
        else make  TLDEPS= all ; fi ) ; fi
make[1]: Entering directory `/home/pepe/src/espresso-5.0.99/GPU/PW'
test -n "" && ( cd ../.. ; make -w  || exit 1) || :
gfortran -O3 -g -fopenmp -x f95-cpp-input -fopenmp -D__GFORTRAN -D__STD_F95
-D__FFTW -D__CUDA -D__PHIGEMM -D__MAGMA -DHAVE_CUBLAS -D__OPENMP
 -I../include -I/home/pepe/src/espresso-5.0.99/GPU/..//qe-magma/include
-I/home/pepe/src/espresso-5.0.99/GPU/..//quark/include
-I/home/pepe/src/espresso-5.0.99/GPU/..//phiGEMM/include
-I/usr/local/cuda-5.5/include -I../../iotk/src -I../../PW/src
-I../../Modules -I../Modules -I.  -c ../../PW/src/pwscf.f90
if [ ! -f ./pwscf.o ]; then cp ../../PW/src/pwscf.o . ; fi
gfortran -g -fopenmp -o pw-gpu.x \
         pwscf.o  ../../PW/src/libpw.a libpwgpu.a ../../Modules/libqemod.a
../Modules/libqemodgpu.a ../../flib/ptools.a ../../flib/flib.a
../../clib/clib.a ../../iotk/src/libiotk.a
 /home/pepe/src/espresso-5.0.99/GPU/..//qe-magma/lib/libmagma.a   -llapack
 -lblas   /home/pepe/src/espresso-5.0.99/GPU/..//phiGEMM/lib/libphigemm.a
-lblas    -L/usr/local/cuda-5.5/lib64 -lcublas  -lcufft -lcudart
/usr/bin/ld:
/home/pepe/src/espresso-5.0.99/GPU/..//qe-magma/lib/libmagma.a(zhetrd_hb2st.o):
undefined reference to symbol '__gxx_personality_v0@@CXXABI_1.3'
/usr/lib/x86_64-linux-gnu/libstdc++.so.6: error adding symbols: DSO missing
from command line
collect2: error: ld returned 1 exit status
make[1]: *** [pw-gpu.x] Error 1
make[1]: Leaving directory `/home/pepe/src/espresso-5.0.99/GPU/PW'
make: *** [pw-gpu] Error 2

In advance, thanks for all your help



On Mon, Apr 7, 2014 at 12:55 PM, PePe <pepe.physics at gmail.com> wrote:

> I have just noticed that during the compilation I get a warning about
> missing include directory
> Warning: Nonexistent include directory
> "/home/pepe/src/espresso-5.0.99/GPU/..//quark/include"
> Where can I find this library?
>
>
> On Mon, Apr 7, 2014 at 12:49 PM, Ari P Seitsonen <Ari.P.Seitsonen at iki.fi>wrote:
>
>>
>> PS Sorry - pardon :
>>
>> make -f Makefile.gpu pw-gpu LD_SHARED_FLAGS=-shared
>>
>>
>> -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=
>> -=*=-=*=-=*=-=*=-
>>   Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/
>>   Institut für Chemie der Universität Zürich, CH-8057 Zürich
>>   Tel: +41 44 63 54 497  /  Mobile: +41 79 71 90 935
>>
>>
>> On Mon, 7 Apr 2014, PePe wrote:
>>
>>  I also have a problem with the compilation. I downloaded
>>> espresso-5.0.99.tar.gz and QE-GPU-14.03.0.tar.gz, placed GPU directory in
>>> espresso main directory (did not apply any patches). Then,
>>> in GPU directory I run:
>>> ./configure --disable-parallel --enable-openmp --enable-cuda
>>> --with-gpu-arch=sm_35 --with-cuda-dir=$CUDA_HOME --with-magma --with-phigemm
>>> cd ..
>>> make -f Makefile.gpu pw-gpu
>>>
>>> the error I get is as follows:
>>>
>>> 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-5.5/lib64 -lcublas  -lcufft -lcudart
>>> /home/pepe/src/espresso-5.0.99/GPU/..//phiGEMM/lib/libphigemm.a
>>> -lblas  -L/usr/local/cuda-5.5/lib64 -lcublas  -lcufft
>>> -lcudart
>>> /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info):
>>> relocation 0 has invalid symbol index 11
>>> /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info):
>>> relocation 1 has invalid symbol index 12
>>> /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info):
>>> relocation 2 has invalid symbol index 2
>>> /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info):
>>> relocation 3 has invalid symbol index 2
>>> /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info):
>>> relocation 4 has invalid symbol index 11
>>> /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info):
>>> relocation 5 has invalid symbol index 13
>>> /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info):
>>> relocation 6 has invalid symbol index 13
>>> /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info):
>>> relocation 7 has invalid symbol index 13
>>> /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info):
>>> relocation 8 has invalid symbol index 12
>>> /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info):
>>> relocation 9 has invalid symbol index 13
>>> /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info):
>>> relocation 10 has invalid symbol index 13
>>> /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info):
>>> relocation 11 has invalid symbol index 13
>>> /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info):
>>> relocation 12 has invalid symbol index 13
>>> /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info):
>>> relocation 13 has invalid symbol index 13
>>> /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info):
>>> relocation 14 has invalid symbol index 13
>>> /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info):
>>> relocation 15 has invalid symbol index 13
>>> /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info):
>>> relocation 16 has invalid symbol index 13
>>> /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info):
>>> relocation 17 has invalid symbol index 13
>>> /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info):
>>> relocation 18 has invalid symbol index 13
>>> /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_info):
>>> relocation 19 has invalid symbol index 21
>>> /usr/bin/ld: /usr/lib/debug/usr/lib/x86_64-linux-gnu/crt1.o(.debug_line):
>>> relocation 0 has invalid symbol index 2
>>> /usr/lib/gcc/x86_64-linux-gnu/4.6/../../../x86_64-linux-gnu/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 `/home/pepe/src/espresso-5.0.99/phiGEMM/src'
>>> make[2]: *** [phigemm] Error 2
>>> make[2]: Leaving directory `/home/pepe/src/espresso-5.0.99/phiGEMM'
>>> make[1]: *** [libphiGEMM] Error 2
>>> make[1]: Leaving directory `/home/pepe/src/espresso-5.0.99/GPU/install'
>>> make: *** [libphiGEMM] Error 2
>>>
>>> Can somebody please help me.
>>>
>>>
>>>
>>> On Sun, Apr 6, 2014 at 1:39 AM, 薛诗川 <nudt.xueshichuan at gmail.com> wrote:
>>>       oh sorry .it seems that i got it , is it espresso-5.0.99.tar.gz?
>>>
>>>       2014-04-06 15:27 GMT+08:00, 薛诗川 <nudt.xueshichuan at gmail.com>:
>>>       > Thank u professor
>>>       > i'll test as soon as possible and tell u the results.
>>>       > but the latest version is 5.0.2,right?
>>>       > when will 5.1 be released?
>>>       >
>>>       > 2014-04-03 11:18 GMT+08:00, 薛诗川 <nudt.xueshichuan at gmail.com>:
>>>       >> dear all,
>>>       >> happy to see that GPU 14.03 has been released, so
>>>       >> i tried to compile it for calculation.
>>>       >> i just followed the instructions in the README file and added
>>> few
>>>       >> manual DFLAGS and make.
>>>       >> but during the process, it failed with such an error:
>>>       >> Fatal error: cannot open mudule file 'mp_bands.mod' for reading.
>>>       >> i cannot figure out its reasons.
>>>       >> need  your help
>>>       >> thanks.
>>>       >>
>>>       >
>>>
>>>       _______________________________________________
>>>       Pw_forum mailing list
>>>       Pw_forum at pwscf.org
>>>       http://pwscf.org/mailman/listinfo/pw_forum
>>>
>>>
>>>
>>>
>> _______________________________________________
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>>
>
>
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