Hi Takanori,
That was it! Thank you very much!
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 21:40, Takanori Nakane wrote:
> Hi,
>
> Please use "cmake -DFORCE_OWN_FLTK=ON".
>
> Best regards,
>
> Takanori Nakane
>
> On 2020/12/01 18:21, Dieter Blaas wrote:
>> 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:
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>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> This message was issued to members of
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>>>>>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>
>>>
>>
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>>
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