Re: compilation with CUDA error

From: Thomas Evangelidis (tevang3_at_gmail.com)
Date: Tue Oct 30 2012 - 02:59:41 CDT

I think I know what the error is, it has to do with the compiler version I
used for CUDA. Because fedora 17 comes with gcc4.7 which is incompatible
with CUDA, I installed from the repositories gcc3.4 and made a symbolic
link at:

ln -s /bin/gcc34 /usr/local/cuda/bin/gcc

Do you know how I can compile CUDA with the Intel compilers to avoid all
this hassle?

T.

On 30 October 2012 09:19, Norman Geist <norman.geist_at_uni-greifswald.de>wrote:

> If I remember correctly and if it hasnít changed yet, namd is not using
> CUDA features of charm++, so you should try to build charm++ without cuda
> support.****
>
> ** **
>
> Norman Geist.****
>
> ** **
>
> *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
> Auftrag von *Aron Broom
> *Gesendet:* Montag, 29. Oktober 2012 18:44
> *An:* Thomas Evangelidis
> *Cc:* namd-l
> *Betreff:* Re: namd-l: compilation with CUDA error****
>
> ** **
>
> it doesn't say anywhere in the instructions which version of cuda it is
> intended for? My impression was that it was 4.0, but that's a big guess.*
> ***
>
> On Mon, Oct 29, 2012 at 9:44 AM, Thomas Evangelidis <tevang3_at_gmail.com>
> wrote:****
>
> Greetings,
>
> I am trying to compile NAMD CVS-2012-09-22_Linux-x86_64-multicore-CUDA
> using Cuda 4.2 with the following command lines:
>
> CUDA_DIR=/usr/local/cuda MAKE=gmake ./build charm++ net-linux-x86_64 icc
> ifort smp cuda -j8 --with-production -O3 -axSSE4.2 -unroll -DCMK_OPTIMIZE=1
> ./config Linux-x86_64-icc --charm-arch net-linux-x86_64-cuda-ifort-smp-icc
> --with-fftw3 --fftw-prefix
> /home/thomas/Programs/fftw-3.3.2/single_precision_Intel_build --cuda-prefix
> /usr/local/cuda
> cd Linux-x86_64-icc
> CUDA_DIR=/usr/local/cuda gmake -j8
>
> but I get the following error:
>
> icpc: command line warning #10121: overriding '-shared-intel' with
> '-i-static'
> icpc: warning #10237: -lcilkrts linked in dynamically, static library not
> available
> .rootdir/charm-6.4.0/net-linux-x86_64-cuda-ifort-smp-icc/bin/../lib/libcudahybridapi.a(hybridapi.o):
> In function `gpuProgressFn':
> tmpxft_00003316_00000000-1_cuda-hybrid-api.cudafe1.cpp:(.text+0xb26):
> undefined reference to `kernelSelect(workRequest*)'
> tmpxft_00003316_00000000-1_cuda-hybrid-api.cudafe1.cpp:(.text+0xbe1):
> undefined reference to `kernelSelect(workRequest*)'
> /usr/local/cuda/lib64/libcudart.so: undefined reference to
> `std::_List_node_base::_M_unhook()@GLIBCXX_3.4.14'
> /usr/local/cuda/lib64/libcudart.so: undefined reference to
> `std::_List_node_base::_M_hook(std::_List_node_base*)@GLIBCXX_3.4.14'
> Fatal Error by charmc in directory
> /home/thomas/Programs/NAMD_CVS-2012-09-22_Source/Linux-x86_64-icc
>
> I also get the same error with Cuda 5.0. I then tried to replace the
> libcudart.so (and libcudart.so.4) with the one that is shipped with NAMD
> but got:
>
> icpc: command line warning #10121: overriding '-shared-intel' with
> '-i-static'
> icpc: warning #10237: -lcilkrts linked in dynamically, static library not
> available
> .rootdir/charm-6.4.0/net-linux-x86_64-cuda-ifort-smp-icc/bin/../lib/libcudahybridapi.a(hybridapi.o):
> In function `gpuProgressFn':
> tmpxft_00003316_00000000-1_cuda-hybrid-api.cudafe1.cpp:(.text+0xb26):
> undefined reference to `kernelSelect(workRequest*)'
> tmpxft_00003316_00000000-1_cuda-hybrid-api.cudafe1.cpp:(.text+0xbe1):
> undefined reference to `kernelSelect(workRequest*)'
> Fatal Error by charmc in directory
> /home/thomas/Programs/NAMD_CVS-2012-09-22_Source/Linux-x86_64-icc
>
> Does anyone know how to fix this? Do I need to install an older version of
> CUDA?
>
> thanks,
> Thomas
>
>
>
> -- ****
>
> ======================================================================****
>
> Thomas Evangelidis****
>
> PhD student****
>
> University of Athens
> Faculty of Pharmacy
> Department of Pharmaceutical Chemistry
> Panepistimioupoli-Zografou
> 157 71 Athens
> GREECE****
>
> email: tevang_at_pharm.uoa.gr****
>
> tevang3_at_gmail.com****
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/****
>
> ** **
>
> ** **
>
>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo****
>

-- 
======================================================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang_at_pharm.uoa.gr
          tevang3_at_gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/

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