Hi,
I took all my courage and updated my system to the latest nvidia driver
and cuda 10.2. It now shows:
nvcc --version
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2019 NVIDIA Corporation
Built on Wed_Oct_23_19:24:38_PDT_2019
Cuda compilation tools, release 10.2, V10.2.89
NVIDIA-SMI 450.66 Driver Version: 450.66 CUDA Version: 11.0
Unfortunately, I get again errors but somewhat different ones. Must the
driver and nvcc have the same version?
[ 76%] Building CXX object
src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o
/opt/RELION/relion-3.1.1/relion/src/gui_mainwindow.cpp: In constructor
‘NoteEditorWindow::NoteEditorWindow(int, int, const char*, FileName, bool)’:
/opt/RELION/relion-3.1.1/relion/src/gui_mainwindow.cpp:220: error:
‘WRAP_AT_BOUNDS’ is not a member of ‘Fl_Text_Display’
/opt/RELION/relion-3.1.1/relion/src/gui_mainwindow.cpp:223: error:
‘class Fl_Text_Buffer’ has no member named ‘transcoding_warning_action’
/opt/RELION/relion-3.1.1/relion/src/gui_mainwindow.cpp: In constructor
‘GuiMainWindow::GuiMainWindow(int, int, const char*, FileName, FileName,
int, int, bool)’:
/opt/RELION/relion-3.1.1/relion/src/gui_mainwindow.cpp:652: error:
‘class Fl_Text_Buffer’ has no member named ‘transcoding_warning_action’
/opt/RELION/relion-3.1.1/relion/src/gui_mainwindow.cpp:653: error:
‘class Fl_Text_Buffer’ has no member named ‘transcoding_warning_action’
/opt/RELION/relion-3.1.1/relion/src/gui_mainwindow.cpp:665: error:
‘WRAP_AT_BOUNDS’ is not a member of ‘Fl_Text_Display’
/opt/RELION/relion-3.1.1/relion/src/gui_mainwindow.cpp:666: error:
‘WRAP_AT_BOUNDS’ is not a member of ‘Fl_Text_Display’
/opt/RELION/relion-3.1.1/relion/src/gui_mainwindow.cpp:944: error:
‘WRAP_AT_BOUNDS’ is not a member of ‘Fl_Text_Display’
/opt/RELION/relion-3.1.1/relion/src/gui_mainwindow.cpp:945: error:
‘WRAP_AT_BOUNDS’ is not a member of ‘Fl_Text_Display’
make[2]: ***
[src/apps/CMakeFiles/relion_gui_lib.dir/__/gui_mainwindow.cpp.o] Error 1
make[1]: *** [src/apps/CMakeFiles/relion_gui_lib.dir/all] Error 2
make: *** [all] Error 2
bw Dieter
------------------------------------------------------------------------
Dieter Blaas,
------------------------------------------------------------------------
Dieter Blaas,
Max Perutz Laboratories
Medical University of Vienna,
Inst. Med. Biochem., Vienna Biocenter (VBC),
Dr. Bohr Gasse 9/3,
A-1030 Vienna, Austria,
Tel: 0043 1 4277 61630,
Mobile: 0043 699 1942 1659
e-mail: [log in to unmask]
------------------------------------------------------------------------
On 01.12.2020 16:48, Takanori Nakane wrote:
> Hi,
>
> Please try 8.0 at least.
>
> Takanori
>
> On 2020/12/01 15:45, Dieter Blaas wrote:
>> Hi,
>>
>> cat /usr/local/cuda/version.txt
>> CUDA Version 7.5.18
>>
>> too old?
>>
>> Dieter
>>
>> ------------------------------------------------------------------------
>> Dieter Blaas,
>> Max Perutz Laboratories
>> Medical University of Vienna,
>> Inst. Med. Biochem., Vienna Biocenter (VBC),
>> Dr. Bohr Gasse 9/3,
>> A-1030 Vienna, Austria,
>> Tel: 0043 1 4277 61630,
>> Mobile: 0043 699 1942 1659
>> e-mail: [log in to unmask]
>> ------------------------------------------------------------------------
>>
>> On 01.12.2020 16:35, Takanori Nakane wrote:
>>> Hi,
>>>
>>> What version of CUDA are you using? Did you specify -DCUDA_ARCH?
>>>
>>> Takanori
>>>
>>> On 2020/12/01 15:31, Dieter Blaas wrote:
>>>> Hi,
>>>>
>>>> Sorry for bothering again! I started again from scratch and
>>>> double checked that I used "git checkout ver3.1" I have surely
>>>> *NOT* set "cmake -DDoublePrec_ACC=ON" and*I also tried "cmake
>>>> -DDoublePrec_ACC=OFF"*. However no avail....
>>>>
>>>> I get the same error messages - any ideas?
>>>>
>>>> bw Dieter
>>>>
>>>> ------------------------------------------------------------------------
>>>>
>>>> Dieter Blaas,
>>>> Max Perutz Laboratories
>>>> Medical University of Vienna,
>>>> Inst. Med. Biochem., Vienna Biocenter (VBC),
>>>> Dr. Bohr Gasse 9/3,
>>>> A-1030 Vienna, Austria,
>>>> Tel: 0043 1 4277 61630,
>>>> Mobile: 0043 699 1942 1659
>>>> e-mail:[log in to unmask]
>>>> ------------------------------------------------------------------------
>>>>
>>>>
>>>> On 01.12.2020 15:20, Takanori Nakane wrote:
>>>>> Hi,
>>>>>
>>>>> > 'git checkout master'
>>>>>
>>>>> But the fix is in the ver3.1 branch. You should check out that.
>>>>>
>>>>> > no instance of overloaded function "atomicAdd" matches the argument
>>>>> > list
>>>>> > argument types are: (double *, double)
>>>>>
>>>>> Didn't you set "cmake -DDoublePrec_ACC=ON"? You should not.
>>>>>
>>>>> Please delete everything in your build directory and
>>>>> start from scratch.
>>>>>
>>>>> Takanori
>>>>>
>>>>> On 2020/12/01 11:40, Dieter Blaas wrote:
>>>>>> Hi Takanori,
>>>>>>
>>>>>> thanks for your effort! I now tried with 'git checkout
>>>>>> master' to exclude newer builds but I now get this:
>>>>>>
>>>>>> [ 66%] Built target relion_lib
>>>>>> [ 67%] Building NVCC (Device) object
>>>>>> src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/cuda_kernels/./relion_gpu_util_generated_helper.cu.o
>>>>>> /opt/RELION/relion-3.1.1/relion/src/acc/cuda/cuda_kernels/helper.cuh(1004):
>>>>>> error: no instance of overloaded function "atomicAdd" matches the
>>>>>> argument list
>>>>>> argument types are: (double *, double)
>>>>>>
>>>>>> /opt/RELION/relion-3.1.1/relion/src/acc/cuda/cuda_kernels/helper.cuh(1005):
>>>>>> error: no instance of overloaded function "atomicAdd" matches the
>>>>>> argument list
>>>>>> argument types are: (double *, double)
>>>>>>
>>>>>> 2 errors detected in the compilation of
>>>>>> "/tmp/tmpxft_000051bd_00000000-5_helper.cpp4.ii".
>>>>>> CMake Error at relion_gpu_util_generated_helper.cu.o.cmake:264
>>>>>> (message):
>>>>>> Error generating file
>>>>>> /opt/RELION/relion-3.1.1/relion/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/cuda_kernels/./relion_gpu_util_generated_helper.cu.o
>>>>>>
>>>>>>
>>>>>>
>>>>>> make[2]: ***
>>>>>> [src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/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
>>>>>>
>>>>>> bw Dieter
>>>>>>
>>>>>> ------------------------------------------------------------------------
>>>>>>
>>>>>> Dieter Blaas,
>>>>>> Max Perutz Laboratories
>>>>>> Medical University of Vienna,
>>>>>> Inst. Med. Biochem., Vienna Biocenter (VBC),
>>>>>> Dr. Bohr Gasse 9/3,
>>>>>> A-1030 Vienna, Austria,
>>>>>> Tel: 0043 1 4277 61630,
>>>>>> Mobile: 0043 699 1942 1659
>>>>>> e-mail: [log in to unmask]
>>>>>> ------------------------------------------------------------------------
>>>>>>
>>>>>>
>>>>>> On 01.12.2020 11:56, Takanori Nakane wrote:
>>>>>>> Hi,
>>>>>>>
>>>>>>> After the fix I made this morning, ver3.1 should work on your
>>>>>>> system. We keep supporting GCC 4.4.x for RELION 3.1.x, but not
>>>>>>> in 3.2 (not-released yet).
>>>>>>>
>>>>>>> Takanori
>>>>>>>
>>>>>>> On 2020/12/01 10:55, Dieter Blaas wrote:
>>>>>>>> Hi,
>>>>>>>>
>>>>>>>> thanks for the hint! What is the very last version that
>>>>>>>> would compile on my system? I do NOT have 3.2 yet! I just used
>>>>>>>> 'checkout ver3.1'
>>>>>>>>
>>>>>>>> bw Dieter
>>>>>>>>
>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>
>>>>>>>> Dieter Blaas,
>>>>>>>> Max Perutz Laboratories
>>>>>>>> Medical University of Vienna,
>>>>>>>> Inst. Med. Biochem., Vienna Biocenter (VBC),
>>>>>>>> Dr. Bohr Gasse 9/3,
>>>>>>>> A-1030 Vienna, Austria,
>>>>>>>> Tel: 0043 1 4277 61630,
>>>>>>>> Mobile: 0043 699 1942 1659
>>>>>>>> e-mail: [log in to unmask]
>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>
>>>>>>>>
>>>>>>>> On 01.12.2020 11:40, Takanori Nakane wrote:
>>>>>>>>> Hi,
>>>>>>>>>
>>>>>>>>> I pushed a change to the ver3.1 branch.
>>>>>>>>> (But I couldn't test it, because this problem does not happen
>>>>>>>>> in a newer compiler)
>>>>>>>>>
>>>>>>>>> Note that we will drop support for your old GCC 4.4.7
>>>>>>>>> in the next major update (3.2). In other words,
>>>>>>>>> RELION 3.2 CANNOT BE COMPILED on your system, unless
>>>>>>>>> you install a newer compiler. This is possible without
>>>>>>>>> root privileges but not trivial (and I cannot teach how to
>>>>>>>>> do this). We will require at least GCC 4.8.x. This is the
>>>>>>>>> default for Cent OS 7 and RHEL 7.
>>>>>>>>>
>>>>>>>>> GCC 4.4.x was the default compiler in Cent OS 6 and RHEL 6 but
>>>>>>>>> lacks full support of C++11 features. Cent OS 6 and
>>>>>>>>> RHEL 6 reached the end of life just yesterday.
>>>>>>>>> https://wiki.centos.org/About/Product
>>>>>>>>> https://en.wikipedia.org/wiki/Red_Hat_Enterprise_Linux#Product_life_cycle
>>>>>>>>>
>>>>>>>>> So it is time to upgrade your system, also for security reasons.
>>>>>>>>>
>>>>>>>>> Best regards,
>>>>>>>>>
>>>>>>>>> Takanori Nakane
>>>>>>>>>
>>>>>>>>> On 2020/12/01 7:40, Dieter Blaas wrote:
>>>>>>>>>> Hi,
>>>>>>>>>>
>>>>>>>>>> I tried installing the very last version of relion-3.1.1
>>>>>>>>>> and got the below error. Is my sytem (Centos-6.10) too old?
>>>>>>>>>> Can anybody please help!
>>>>>>>>>>
>>>>>>>>>> Thanks a lot, best, Dieter
>>>>>>>>>>
>>>>>>>>>> make
>>>>>>>>>> Scanning dependencies of target copy_scripts
>>>>>>>>>> [ 0%] Built target copy_scripts
>>>>>>>>>> Scanning dependencies of target relion_lib
>>>>>>>>>> [ 1%] Building CXX object
>>>>>>>>>> src/apps/CMakeFiles/relion_lib.dir/__/pipeline_jobs.cpp.o
>>>>>>>>>> [ 1%] Building CXX object
>>>>>>>>>> src/apps/CMakeFiles/relion_lib.dir/__/memory.cpp.o
>>>>>>>>>> [ 2%] Building CXX object
>>>>>>>>>> src/apps/CMakeFiles/relion_lib.dir/__/image.cpp.o
>>>>>>>>>> [ 2%] Building CXX object
>>>>>>>>>> src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner.cpp.o
>>>>>>>>>> [ 3%] Building CXX object
>>>>>>>>>> src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o
>>>>>>>>>>
>>>>>>>>>> [ 3%] Building CXX object
>>>>>>>>>> src/apps/CMakeFiles/relion_lib.dir/__/metadata_table.cpp.o
>>>>>>>>>> /opt/RELION/relion-3.1.1/relion/src/metadata_table.cpp: In
>>>>>>>>>> member function \u2018void MetaDataTable::addLabel(EMDLabel,
>>>>>>>>>> std::string)\u2019:
>>>>>>>>>> /opt/RELION/relion-3.1.1/relion/src/metadata_table.cpp:620:
>>>>>>>>>> error: call of overloaded \u2018to_string(EMDLabel&)\u2019 is
>>>>>>>>>> ambiguous
>>>>>>>>>> /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h:2604:
>>>>>>>>>> note: candidates are: std::string std::to_string(long long int)
>>>>>>>>>> /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h:2610:
>>>>>>>>>> note: std::string std::to_string(long long
>>>>>>>>>> unsigned int)
>>>>>>>>>> /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h:2616:
>>>>>>>>>> note: std::string std::to_string(long double)
>>>>>>>>>> make[2]: ***
>>>>>>>>>> [src/apps/CMakeFiles/relion_lib.dir/__/metadata_table.cpp.o]
>>>>>>>>>> Error 1
>>>>>>>>>> make[1]: *** [src/apps/CMakeFiles/relion_lib.dir/all] Error 2
>>>>>>>>>>
>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>>
>>>>>>>>>> Dieter Blaas,
>>>>>>>>>> Max Perutz Laboratories
>>>>>>>>>> Medical University of Vienna,
>>>>>>>>>> Inst. Med. Biochem., Vienna Biocenter (VBC),
>>>>>>>>>> Dr. Bohr Gasse 9/3,
>>>>>>>>>> A-1030 Vienna, Austria,
>>>>>>>>>> Tel: 0043 1 4277 61630,
>>>>>>>>>> Mobile: 0043 699 1942 1659
>>>>>>>>>> e-mail: [log in to unmask]
>>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> ########################################################################
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> To unsubscribe from the CCPEM list, click the following link:
>>>>>>>>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCPEM&A=1
>>>>>>>>>>
>>>>>>>>>> This message was issued to members of
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>>>>>>>>>
>>>>>>>
>>>>>
>>>
>
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