I am trying to do a fresh install of CryoSparc, and while I am able to install the cryosparc_master, I am not able to install the cryosparc_worker. When I try to run a cryosparc_worker install, i get the following error message about halfway through:
And then I get this error at the end:
I know that the /usr/bin/gcc failed with exit code 1 means that it doesn’t think gcc is installed, but it is.
So I then tried to install the python-devel packages, and those are all up to date.
Then I updated pip, which didn’t solve the problem either.
Finally, I specified the CUDA path, which also didn’t fix the problem.
Any ideas on how to fix this would be greatly appreciated.
Here is information about my workstation:
after running echo $PATH
Running whereis cuda:
nvidia-smi
Please post the error messages as text to make questions on this forum more “findable”.
What is the version of your CUDA toolkit:
/usr/local/cuda/bin/nvcc --version
?
CUDA-11.8 is currently the latest version supported by CryoSPARC.
type or paste /usr/local/cuda/bin/nvcc --version
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2023 NVIDIA Corporation
Built on Tue_Feb__7_19:32:13_PST_2023
Cuda compilation tools, release 12.1, V12.1.66
Build cuda_12.1.r12.1/compiler.32415258_0
code here
Welp, I think that’s my issue. Though when I was downloading it from Nvidia, it looked like I was downloading 11.7.
This is what I had installed before though, so I’m not sure if I should be changing something in the commands?
wget https://developer.download.nvidia.com/compute/cuda/11.7.0/local_installers/cuda-repo-rhel7-11-7-local-11.7.0_515.43.04-1.x86_64.rpm
sudo rpm -i cuda-repo-rhel7-11-7-local-11.7.0_515.43.04-1.x86_64.rpm
sudo yum clean all
sudo yum -y install nvidia-driver-latest-dkms cuda
sudo yum -y install cuda-drivers
Your CryoSPARC installation may be more stable if you install the toolkit as part of
cryosparcw install-3dflex, but ensure the prerequisites of that installation method.
I already have that downloaded. I’m not sure what’s happening but when I run install cuda, it will only install 12.1 no matter what I download:
* updates: mirror.team-cymru.com
base | 3.6 kB 00:00:00
centos-sclo-rh | 3.0 kB 00:00:00
centos-sclo-sclo | 3.0 kB 00:00:00
cuda-rhel7-11-7-local | 3.0 kB 00:00:00
cuda-rhel7-11-8-local | 3.0 kB 00:00:00
cuda-rhel7-x86_64 | 3.0 kB 00:00:00
epel | 4.7 kB 00:00:00
extras | 2.9 kB 00:00:00
updates | 2.9 kB 00:00:00
(1/12): cuda-rhel7-11-7-local/primary_db | 56 kB 00:00:00
(2/12): cuda-rhel7-11-8-local/primary_db | 57 kB 00:00:00
(3/12): base/7/x86_64/group_gz | 153 kB 00:00:00
(4/12): centos-sclo-sclo/x86_64/primary_db | 300 kB 00:00:00
(5/12): base/7/x86_64/primary_db | 6.1 MB 00:00:00
(6/12): cuda-rhel7-x86_64/primary_db | 1.9 MB 00:00:00
(7/12): epel/x86_64/group_gz | 99 kB 00:00:00
(8/12): epel/x86_64/updateinfo | 1.0 MB 00:00:00
(9/12): centos-sclo-rh/x86_64/primary_db | 3.4 MB 00:00:00
(10/12): epel/x86_64/primary_db | 7.0 MB 00:00:00
(11/12): extras/7/x86_64/primary_db | 249 kB 00:00:00
(12/12): updates/7/x86_64/primary_db | 20 MB 00:00:00
No package nvidia-drivers-latest-dkms available.
Error: Nothing to do
$ sudo yum -y install cuda
Loaded plugins: fastestmirror, langpacks, nvidia
Loading mirror speeds from cached hostfile
* base: mirror.grid.uchicago.edu
* centos-sclo-rh: atl.mirrors.clouvider.net
* centos-sclo-sclo: mirror.grid.uchicago.edu
* epel: ftp-chi.osuosl.org
* extras: mirror.cs.uwp.edu
* updates: mirror.team-cymru.com
Package cuda-12.1.0-1.x86_64 already installed and latest version
Nothing to do
I’ve tried every which way to uninstall it by this point.
With 3DFlex prerequisites installed, a “system-wide”, installation of the CUDA toolkit is not required for CryoSPARC function. Under certain circumstances, presence of “system-wide” toolkit components in PATH or LD_LIBRARY_PATH definitions may interfere with the installation and use of 3DFlex prerequisites.
A possible workaround may be to
- not install a “system-wide” toolkit
- install versions of the toolkit as needed by various software packages without “globally” including any toolkit installation in
PATH or LD_LIBRARY_PATH definitions. To avoid inadvertent system-wide configuration changes, the “runfile” of the toolkit can be installed by a non-root user with the --toolkit, --toolkitpath=, --defaultroot= parameters.
