Thanks a lot! The installation finished without error with this modification.
Best,
Nicolas
________________________________________
From: Hattne, Johan [[log in to unmask]]
Sent: Thursday, December 22, 2016 12:38 PM
To: Coudray, Nicolas
Cc: [log in to unmask]
Subject: Re: [ccpem] "nvcc fatal" error during installation on Centos 6.8
No, that won’t work. The quotes I had in mind are in CMake’s run_nvcc.cmake (/usr/share/cmake/Modules/FindCUDA/run_nvcc.cmake on the system I’m currently on). Change the line that reads
set(CUDA_NVCC_COMPILE_DEFINITIONS "@CUDA_NVCC_COMPILE_DEFINITIONS@") # list (needs to be in quotes to handle spaces properly).
into
set(CUDA_NVCC_COMPILE_DEFINITIONS @CUDA_NVCC_COMPILE_DEFINITIONS@) # list (needs to be in quotes to handle spaces properly).
Spaces appear to be handled properly even without the quotes.
// Cheers; Johan
> On Dec 22, 2016, at 11:55, Coudray, Nicolas <[log in to unmask]> wrote:
>
> Thanks for the suggestion Johan. I removed the quotes in lines 19 & 20 of the RELION's CMakeLists.txt file:
>
> add_definitions(-DINSTALL_LIBRARY_DIR=${CMAKE_INSTALL_PREFIX}/lib/)
> add_definitions(-DSOURCE_DIR=${CMAKE_SOURCE_DIR}/src/)
>
> This indeed does not generate the nvcc error anymore, but another occurs a bit later:
>
> [ 23%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/gui_mainwindow.cpp.o
> /ifs/data/cryoem/relion-2.0/relion2-beta_t/src/gui_mainwindow.cpp: In constructor \u2018RelionMainWindow::RelionMainWindow(int, int, const char*, FileName, int, int, bool)\u2019:
> /ifs/data/cryoem/relion-2.0/relion2-beta_t/src/gui_mainwindow.cpp:280: error: \u2018usr\u2019 was not declared in this scope
> /ifs/data/cryoem/relion-2.0/relion2-beta_t/src/gui_mainwindow.cpp:280: error: \u2018local\u2019 was not declared in this scope
> /ifs/data/cryoem/relion-2.0/relion2-beta_t/src/gui_mainwindow.cpp:280: error: \u2018lib\u2019 was not declared in this scope
> /ifs/data/cryoem/relion-2.0/relion2-beta_t/src/gui_mainwindow.cpp:280: error: expected primary-expression before \u2018(\u2019 token
> /ifs/data/cryoem/relion-2.0/relion2-beta_t/src/gui_mainwindow.cpp:280: error: expected primary-expression before \u2018/\u2019 token
> /ifs/data/cryoem/relion-2.0/relion2-beta_t/src/gui_mainwindow.cpp:280: error: expected primary-expression before \u2018)\u2019 token
> /ifs/data/cryoem/relion-2.0/relion2-beta_t/src/gui_mainwindow.cpp:284: error: \u2018ifs\u2019 was not declared in this scope
> /ifs/data/cryoem/relion-2.0/relion2-beta_t/src/gui_mainwindow.cpp:284: error: \u2018data\u2019 was not declared in this scope
> /ifs/data/cryoem/relion-2.0/relion2-beta_t/src/gui_mainwindow.cpp:284: error: \u2018cryoem\u2019 was not declared in this scope
> /ifs/data/cryoem/relion-2.0/relion2-beta_t/src/gui_mainwindow.cpp:284: error: \u2018relion\u2019 was not declared in this scope
> /ifs/data/cryoem/relion-2.0/relion2-beta_t/src/gui_mainwindow.cpp:284: error: \u2018relion2\u2019 was not declared in this scope
> /ifs/data/cryoem/relion-2.0/relion2-beta_t/src/gui_mainwindow.cpp:284: error: \u2018beta_t\u2019 was not declared in this scope
> /ifs/data/cryoem/relion-2.0/relion2-beta_t/src/gui_mainwindow.cpp:284: error: \u2018src\u2019 was not declared in this scope
> /ifs/data/cryoem/relion-2.0/relion2-beta_t/src/gui_mainwindow.cpp:284: error: expected primary-expression before \u2018(\u2019 token
> /ifs/data/cryoem/relion-2.0/relion2-beta_t/src/gui_mainwindow.cpp:284: error: expected primary-expression before \u2018/\u2019 token
> /ifs/data/cryoem/relion-2.0/relion2-beta_t/src/gui_mainwindow.cpp:284: error: expected primary-expression before \u2018)\u2019 token
> make[2]: *** [src/apps/CMakeFiles/relion_lib.dir/__/gui_mainwindow.cpp.o] Error 1
> make[1]: *** [src/apps/CMakeFiles/relion_lib.dir/all] Error 2
> make: *** [all] Error 2
>
>
> ________________________________________
>
> From: Hattne, Johan [[log in to unmask]]
> Sent: Thursday, December 22, 2016 11:19 AM
> To: Coudray, Nicolas
> Cc: [log in to unmask]
> Subject: Re: [ccpem] "nvcc fatal" error during installation on Centos 6.8
>
> See
>
>
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__gitlab.kitware.com_cmake_cmake_issues_16510&d=DgIGaQ&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=RRJopfWEMpjEmb1q4aEqzyQjd97NtX3Xt1ANiQcXoKc&m=NzUWz3pym1dcZWJEyKd4l3opSyyZHqvnCKPyu7AZFvY&s=JaLjAZQHIYkmemrns2EoS0yhW737Z9NobWcM5sqR-zU&e=
>
>
>
> Removing the quotes in CMake’s run_nvcc.cmake works for me, but I don’t know enough CMake to tell whether this is really The Right Thing to do. If you do not have sufficient permission to edit that file, you can also work around the issue by modifying the RELION sources; I could send a patch for that anyone's interested.
>
>
>
> // Johan
>
>
>
> > On Dec 22, 2016, at 11:02, Coudray, Nicolas <[log in to unmask]> wrote:
>
> >
>
> > Hi All,
>
> >
>
> > We're trying to install RELION on a cluster (CENTOS 6.8) but are runinng into this error when running the make command:
>
> >
>
> > [ 0%] Built target copy_scripts
>
> > [ 1%] Building NVCC (Device) object src/apps/CMakeFiles/relion_gpu_util.dir/__/gpu_utils/cuda_kernels/relion_gpu_util_generated_helper.cu.o
>
> > CMake Warning (dev) at relion_gpu_util_generated_helper.cu.o.Release.cmake:81:
>
> > Syntax Warning in cmake code at column 57
>
> > Argument not separated from preceding token by whitespace.
>
> > This warning is for project developers. Use -Wno-dev to suppress it.
>
> > nvcc fatal : Stray '"' character
>
> > CMake Error at relion_gpu_util_generated_helper.cu.o.Release.cmake:222 (message):
>
> > Error generating
>
> > /ifs/data/cryoem/relion-2.0/relion2-beta_t/build2/src/apps/CMakeFiles/relion_gpu_util.dir/__/gpu_utils/cuda_kernels/./relion_gpu_util_generated_helper.cu.o
>
> > make[2]: *** [src/apps/CMakeFiles/relion_gpu_util.dir/__/gpu_utils/cuda_kernels/relion_gpu_util_generated_helper.cu.o] Error 1
>
> > make[1]: *** [src/apps/CMakeFiles/relion_gpu_util.dir/all] Error 2
>
> > make: *** [all] Error 2
>
> >
>
> > Other information about the system:
>
> > * We're using cmake/3.7.1 and openmpi 1.10.1
>
> > * GNU 4.4.7
>
> > * ldd (GNU libc) 2.12
>
> >
>
> > Does anyone know what the error is and how to solve this?
>
> >
>
> >
>
> > Thanks,
>
> >
>
> > Nicolas Coudray
>
> > New York University
>
> >
>
> >
>
> >
>
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> > =================================
>
>
>
> Research Specialist @ Gonen Lab
>
> ____________________________________________________
>
> Janelia Research Campus * 19700 Helix Drive
>
> Ashburn, VA 20147 * +1 (571) 209-4000 extension 3376
>
>
>
>
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Research Specialist @ Gonen Lab
____________________________________________________
Janelia Research Campus * 19700 Helix Drive
Ashburn, VA 20147 * +1 (571) 209-4000 extension 3376
------------------------------------------------------------
This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.
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