From: Thomas Evangelidis (tevang3_at_gmail.com)
Date: Mon Oct 29 2012 - 08:44:23 CDT
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/
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