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3dem / relion

Image-processing software for cryo-electron microscopy
https://relion.readthedocs.io/en/latest/
GNU General Public License v2.0
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Installation issue #1132

Open nwaxham opened 3 months ago

nwaxham commented 3 months ago

Describe your problem

Installation failing. There is nothing else installed on this workstation other than the ubuntu os. This attempt at installing relion is the first package I'm attempting to install.

Environment:

Running into a persistent problem installing relion v5 (or v4) on a fresh install of ubuntu 22.04.04 during the make -j command.

The call works, but each time hits the same error and exits. Seems GPU related nvcc --version returns: Cuda compilation tools, release 11.5, V11.5.119 Build cuda_11.5.r11.5/compiler.30672275_0

Specific error, copied from terminal (original appears in red): /usr/include/c++/11/bits/std_function.h:530:146: note: ‘_ArgTypes’ CMake Error at relion_gpu_util_generated_cuda_projector_plan.cu.o.Release.cmake:280 (message): Error generating file /home/neal/relion/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_projector_plan.cu.o

make[2]: [src/apps/CMakeFiles/relion_gpu_util.dir/build.make:4698: src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_projector_plan.cu.o] Error 1 make[1]: [CMakeFiles/Makefile2:381: src/apps/CMakeFiles/relion_gpu_util.dir/all] Error 2 make: *** [Makefile:136: all] Error 2

Any insights would be welcomed.

Thanks. Neal.

biochem-fan commented 3 months ago

/usr/include/c++/11/bits/std_function.h:530:146: note: ‘_ArgTypes’

This looks like an incompatibility of CUDA and GCC. Can you try a newer CUDA SDK that natively supports Ubuntu 22.04 LTS?

nwaxham commented 3 months ago

Installed are the newest versions of the cuda driver and the cuda toolkit

cuda-repo-ubuntu2204-12-5-local_12.5.0-555.42.02-1_amd64 cuda-toolkit-12-5 is already the newest version (12.5.0-1).

biochem-fan commented 3 months ago

nvcc --version returns: Cuda compilation tools, release 11.5, V11.5.119 Build cuda_11.5.r11.5/compiler.30672275_0

But this says 11.5. Aren't you building RELION within a conda environment?

nwaxham commented 3 months ago

agreed, just discovered that also.
when I run sudo apt-get -y install cuda-toolkit-12-5 it returns cuda-toolkit-12-5 is already the newest version (12.5.0-1). but nvcc --version returns: Cuda compilation tools, release 11.5, V11.5.119 Build cuda_11.5.r11.5/compiler.30672275_0

It's like the install is not over writing the resident 11.5 version. N.

biochem-fan commented 3 months ago

Your PATH is wrong.

nwaxham commented 3 months ago

BTW, I do NOT activate the conda environment for the make and build steps, the instructions say not to do that. I'm doing the installation with conda deactivate.

biochem-fan commented 3 months ago

BTW, I do NOT activate the conda environment for the make and build steps, the instructions say not to do that. I'm doing the installation with conda deactivate.

Great. Then the old CUDA is coming from somewhere else. Check which nvcc and amend the PATH.

nwaxham commented 3 months ago

Thanks. which nvcc returns /usr/bin/nvcc. /usr/bin is already in the path.

biochem-fan commented 3 months ago

What installed the old CUDA?

You wrote

This attempt at installing relion is the first package I'm attempting to install.

and you did

sudo apt-get -y install cuda-toolkit-12-5

but clearly something else has installed the old CUDA.

This is not a RELION issue but your system issue so I cannot help further. Please sort it out yourself.

nwaxham commented 3 months ago

Affirm.

Neal Waxham, Ph.D. Professor of Neurobiology and Anatomy McGovern Medical School Houston, TX 77030 https://sites.google.com/uth.edu/waxham-lab/home

From: biochem_fan @.> Date: Friday, May 24, 2024 at 7:07 PM To: 3dem/relion @.> Cc: Waxham, M Neal @.>, Author @.> Subject: Re: [3dem/relion] Installation issue (Issue #1132) External: Increase caution when handling links and attachments.

What installed the old CUDA?

You wrote

This attempt at installing relion is the first package I'm attempting to install.

and you did

sudo apt-get -y install cuda-toolkit-12-5

but clearly something else has installed the old CUDA.

This is not a RELION issue but your system issue so I cannot help further. Please sort it out yourself.

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nwaxham commented 3 months ago

Some progress. Cuda problem corrected. This is on Ubuntu 22.04.

A question about the GUI that requires FLTK. It is not clear if FLTK is installed with the command: sudo apt install cmake git build-essential mpi-default-bin mpi-default-dev libfftw3-dev libtiff-dev libpng-dev ghostscript libxft-dev Does FLTK need installed separately before running cmake?

biochem-fan commented 3 months ago

No. RELION will download and build FLTK itself. If this does not work, please add -DFORCE_OWN_FLTK=ON to cmake.