RosettaCommons
Provide the SIF file
Could you provide the SIF file used by Singularity? It's difficult to install on some HPCs. Thank you.
I created a def file. you may build the sif by yourself.
https://github.com/Masterchiefm/apptainer-protein-science/tree/main/foundry
I created a def file. you may build the sif by yourself.
https://github.com/Masterchiefm/apptainer-protein-science/tree/main/foundry
If you have some free time, could you please help me build a SIF file? Thank you very much for considering my question.
I created a def file. you may build the sif by yourself. https://github.com/Masterchiefm/apptainer-protein-science/tree/main/foundry
If you have some free time, could you please help me build a SIF file? Thank you very much for considering my question.
Please directly state the problem you are encountering. This kind of probing question only wastes both of our time.
I created a def file. you may build the sif by yourself. https://github.com/Masterchiefm/apptainer-protein-science/tree/main/foundry
If you have some free time, could you please help me build a SIF file? Thank you very much for considering my question.
My command: conda create -n RFdiffusion3_env_312_3 python=3.12 conda activate RFdiffusion3_env_312_3 conda install -c conda-forge gcc_linux-64 gxx_linux-64 export CC=$CONDA_PREFIX/bin/x86_64-conda-linux-gnu-gcc export CXX=$CONDA_PREFIX/bin/x86_64-conda-linux-gnu-g++ conda install -c conda-forge go export WANDB_BUILD_SKIP_GPU_STATS=true pip install wandb --no-cache-dir pip install rc-foundry[all]
Command error: Collecting rc-foundry[all] Downloading https://pypi.tuna.tsinghua.edu.cn/packages/aa/cc/3f06d28375c515535c63d2e2ca15ac69370de638859b20389005b85811c6/rc_foundry-0.1.6-py3-none-any.whl (613 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 614.0/614.0 kB 7.7 MB/s 0:00:00 Downloading https://pypi.tuna.tsinghua.edu.cn/packages/d0/27/c621238d9995de1411b08917e2d1eed44b81be0616eb82c070bffa0edc9f/rc_foundry-0.1.5-py3-none-any.whl (545 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 545.2/545.2 kB 4.8 MB/s 0:00:00 Downloading https://pypi.tuna.tsinghua.edu.cn/packages/4b/51/7885547733e3191b82d7d245fa9f9d2d46ae44753215ab5172801fa72248/rc_foundry-0.1.4-py3-none-any.whl (545 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 545.4/545.4 kB 848.1 kB/s 0:00:00 Downloading https://pypi.tuna.tsinghua.edu.cn/packages/e4/59/1e08d10459949517fd6bfd07d694156e58c3caf7629dd26539486ab900a1/rc_foundry-0.1.3-py3-none-any.whl (545 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 545.4/545.4 kB 6.1 MB/s 0:00:00 Downloading https://pypi.tuna.tsinghua.edu.cn/packages/d9/fe/27efdc4a887136b710234bd2af79a5578d47558cd4127915717a1f94da7c/rc_foundry-0.1.2-py3-none-any.whl (545 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 545.4/545.4 kB 6.0 MB/s 0:00:00 Downloading https://pypi.tuna.tsinghua.edu.cn/packages/22/0f/8b26a779b38508f57a4e1f3df552773ae0d4a701d600ae8e96da3d2b4c82/rc_foundry-0.1.1-py3-none-any.whl (545 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 545.5/545.5 kB 2.1 MB/s 0:00:00 ERROR: Cannot install rc-foundry[all]==0.1.1, rc-foundry[all]==0.1.2, rc-foundry[all]==0.1.3, rc-foundry[all]==0.1.4, rc-foundry[all]==0.1.5, rc-foundry[all]==0.1.6 and rc-foundry[all]==0.1.7 because these package versions have conflicting dependencies.
The conflict is caused by: rc-foundry[all] 0.1.7 depends on cuequivariance-ops-cu12>=0.6.1; sys_platform == "linux" and extra == "all" rc-foundry[all] 0.1.6 depends on cuequivariance-ops-cu12>=0.6.1; sys_platform == "linux" and extra == "all" rc-foundry[all] 0.1.5 depends on cuequivariance-ops-cu12>=0.6.1; sys_platform == "linux" and extra == "all" rc-foundry[all] 0.1.4 depends on cuequivariance-ops-cu12>=0.6.1; sys_platform == "linux" and extra == "all" rc-foundry[all] 0.1.3 depends on cuequivariance-ops-cu12>=0.6.1; sys_platform == "linux" and extra == "all" rc-foundry[all] 0.1.2 depends on cuequivariance-ops-cu12>=0.6.1; sys_platform == "linux" and extra == "all" rc-foundry[all] 0.1.1 depends on cuequivariance-ops-cu12>=0.6.1; sys_platform == "linux" and extra == "all"
Additionally, some packages in these conflicts have no matching distributions available for your environment: cuequivariance-ops-cu12
To fix this you could try to:
- loosen the range of package versions you've specified
- remove package versions to allow pip to attempt to solve the dependency conflict
ERROR: ResolutionImpossible: for help visit https://pip.pypa.io/en/latest/topics/dependency-resolution/#dealing-with-dependency-conflicts
In addition, I am an HPC user without sudo privileges, which makes it very difficult for me to build the SIF files needed to run Singularity on my own.
From: rockylinux/rockylinux:9.6
%files
path_to_hbplus/hbplus /hbplus
path_to_foundry/foundry /foundry
%post
# base os
yum install -y wget git gcc-gfortran gcc gcc-c++ kernel-devel make
cd /hbplus
make
cd ../
# install miniconda
wget https://repo.anaconda.com/archive/Anaconda3-2024.10-1-Linux-x86_64.sh
bash Anaconda3-2024.10-1-Linux-x86_64.sh -b -f -p /opt/conda
rm Anaconda3-2024.10-1-Linux-x86_64.sh
# install conda components - add the packages you need here
. /opt/conda/etc/profile.d/conda.sh
export PATH=/opt/conda/bin:$PATH
conda create -n foundry python=3.12
conda activate foundry
pip install uv
uv pip install rc-foundry==0.1.7
foundry install base-models --checkpoint-dir /opt/checkpoints
echo -e "#! /bin/bash\n\n# script to activate the conda environment" > ~/.bashrc
conda init bash
echo -e "\nconda activate foundry" >> ~/.bashrc
conda update --all
mkdir /opt/etc
cp ~/.bashrc /opt/etc/bashrc
cp -r /foundry/models/rf3/configs /opt/conda/envs/foundry/lib/python3.12/
%environment
export PATH=/opt/conda/bin:/hbplus:$PATH
source /opt/etc/bashrc
%labels
Author Dhiraj Srivastava
RFdiffusion is working but RF is showing error as described in #94 39,1 Bot
I created a def file. you may build the sif by yourself. https://github.com/Masterchiefm/apptainer-protein-science/tree/main/foundry
If you have some free time, could you please help me build a SIF file? Thank you very much for considering my question.
My command: conda create -n RFdiffusion3_env_312_3 python=3.12 conda activate RFdiffusion3_env_312_3 conda install -c conda-forge gcc_linux-64 gxx_linux-64 export CC=$CONDA_PREFIX/bin/x86_64-conda-linux-gnu-gcc export CXX=$CONDA_PREFIX/bin/x86_64-conda-linux-gnu-g++ conda install -c conda-forge go export WANDB_BUILD_SKIP_GPU_STATS=true pip install wandb --no-cache-dir pip install rc-foundry[all]
Command error: Collecting rc-foundry[all] Downloading https://pypi.tuna.tsinghua.edu.cn/packages/aa/cc/3f06d28375c515535c63d2e2ca15ac69370de638859b20389005b85811c6/rc_foundry-0.1.6-py3-none-any.whl (613 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 614.0/614.0 kB 7.7 MB/s 0:00:00 Downloading https://pypi.tuna.tsinghua.edu.cn/packages/d0/27/c621238d9995de1411b08917e2d1eed44b81be0616eb82c070bffa0edc9f/rc_foundry-0.1.5-py3-none-any.whl (545 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 545.2/545.2 kB 4.8 MB/s 0:00:00 Downloading https://pypi.tuna.tsinghua.edu.cn/packages/4b/51/7885547733e3191b82d7d245fa9f9d2d46ae44753215ab5172801fa72248/rc_foundry-0.1.4-py3-none-any.whl (545 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 545.4/545.4 kB 848.1 kB/s 0:00:00 Downloading https://pypi.tuna.tsinghua.edu.cn/packages/e4/59/1e08d10459949517fd6bfd07d694156e58c3caf7629dd26539486ab900a1/rc_foundry-0.1.3-py3-none-any.whl (545 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 545.4/545.4 kB 6.1 MB/s 0:00:00 Downloading https://pypi.tuna.tsinghua.edu.cn/packages/d9/fe/27efdc4a887136b710234bd2af79a5578d47558cd4127915717a1f94da7c/rc_foundry-0.1.2-py3-none-any.whl (545 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 545.4/545.4 kB 6.0 MB/s 0:00:00 Downloading https://pypi.tuna.tsinghua.edu.cn/packages/22/0f/8b26a779b38508f57a4e1f3df552773ae0d4a701d600ae8e96da3d2b4c82/rc_foundry-0.1.1-py3-none-any.whl (545 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 545.5/545.5 kB 2.1 MB/s 0:00:00 ERROR: Cannot install rc-foundry[all]==0.1.1, rc-foundry[all]==0.1.2, rc-foundry[all]==0.1.3, rc-foundry[all]==0.1.4, rc-foundry[all]==0.1.5, rc-foundry[all]==0.1.6 and rc-foundry[all]==0.1.7 because these package versions have conflicting dependencies.
The conflict is caused by: rc-foundry[all] 0.1.7 depends on cuequivariance-ops-cu12>=0.6.1; sys_platform == "linux" and extra == "all" rc-foundry[all] 0.1.6 depends on cuequivariance-ops-cu12>=0.6.1; sys_platform == "linux" and extra == "all" rc-foundry[all] 0.1.5 depends on cuequivariance-ops-cu12>=0.6.1; sys_platform == "linux" and extra == "all" rc-foundry[all] 0.1.4 depends on cuequivariance-ops-cu12>=0.6.1; sys_platform == "linux" and extra == "all" rc-foundry[all] 0.1.3 depends on cuequivariance-ops-cu12>=0.6.1; sys_platform == "linux" and extra == "all" rc-foundry[all] 0.1.2 depends on cuequivariance-ops-cu12>=0.6.1; sys_platform == "linux" and extra == "all" rc-foundry[all] 0.1.1 depends on cuequivariance-ops-cu12>=0.6.1; sys_platform == "linux" and extra == "all"
Additionally, some packages in these conflicts have no matching distributions available for your environment: cuequivariance-ops-cu12
To fix this you could try to:
- loosen the range of package versions you've specified
- remove package versions to allow pip to attempt to solve the dependency conflict
ERROR: ResolutionImpossible: for help visit https://pip.pypa.io/en/latest/topics/dependency-resolution/#dealing-with-dependency-conflicts
In addition, I am an HPC user without sudo privileges, which makes it very difficult for me to build the SIF files needed to run Singularity on my own.
I don't understand why you install so many unnecessary packages and set many variables.
Simply using the following 3 commands is enough:
conda create -n fondry python=3.12
conda activate fondry
pip install "rc-foundry[all]"
HPC user can build a singlarity image. Once you got a def file, you can build it by yourself.
If you mean you cannot build sif in HPC, you may misunderstand how singularity works.
You need to build the sif on your local PC, then you can get a sif file, and copy it to HPC
In HPC, your script may include something like the following:
#!/bin/bash
#PBS -N jobnane
#PBS -l nodes=1:ppn=1
#PBS -q siais_gpu_5
#PBS -l walltime=80:00:00
#PBS -o log.out
#PBS -e log.err
module load cuda/7/12.2
module load apps/7/singularity/3.5.2
singularity run --nv \
-B cache:/cache \
-B workdir:/workdir \
image.sif \ # this sif file is built in your PC.
script
From: rockylinux/rockylinux:9.6 %files path_to_hbplus/hbplus /hbplus path_to_foundry/foundry /foundry %post # base os yum install -y wget git gcc-gfortran gcc gcc-c++ kernel-devel make cd /hbplus make cd ../ # install miniconda wget https://repo.anaconda.com/archive/Anaconda3-2024.10-1-Linux-x86_64.sh bash Anaconda3-2024.10-1-Linux-x86_64.sh -b -f -p /opt/conda rm Anaconda3-2024.10-1-Linux-x86_64.sh # install conda components - add the packages you need here . /opt/conda/etc/profile.d/conda.sh export PATH=/opt/conda/bin:$PATH conda create -n foundry python=3.12 conda activate foundry pip install uv uv pip install rc-foundry==0.1.7 foundry install base-models --checkpoint-dir /opt/checkpoints echo -e "#! /bin/bash\n\n# script to activate the conda environment" > ~/.bashrc conda init bash echo -e "\nconda activate foundry" >> ~/.bashrc conda update --all mkdir /opt/etc cp ~/.bashrc /opt/etc/bashrc cp -r /foundry/models/rf3/configs /opt/conda/envs/foundry/lib/python3.12/ %environment export PATH=/opt/conda/bin:/hbplus:$PATH source /opt/etc/bashrc %labels Author Dhiraj SrivastavaRFdiffusion is working but RF is showing error as described in #94 39,1 Bot
Same as me: https://github.com/RosettaCommons/foundry/issues/100#issuecomment-3655453818
I created a def file. you may build the sif by yourself. https://github.com/Masterchiefm/apptainer-protein-science/tree/main/foundry
If you have some free time, could you please help me build a SIF file? Thank you very much for considering my question.
My command: conda create -n RFdiffusion3_env_312_3 python=3.12 conda activate RFdiffusion3_env_312_3 conda install -c conda-forge gcc_linux-64 gxx_linux-64 export CC=$CONDA_PREFIX/bin/x86_64-conda-linux-gnu-gcc export CXX=$CONDA_PREFIX/bin/x86_64-conda-linux-gnu-g++ conda install -c conda-forge go export WANDB_BUILD_SKIP_GPU_STATS=true pip install wandb --no-cache-dir pip install rc-foundry[all] Command error: Collecting rc-foundry[all] Downloading https://pypi.tuna.tsinghua.edu.cn/packages/aa/cc/3f06d28375c515535c63d2e2ca15ac69370de638859b20389005b85811c6/rc_foundry-0.1.6-py3-none-any.whl (613 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 614.0/614.0 kB 7.7 MB/s 0:00:00 Downloading https://pypi.tuna.tsinghua.edu.cn/packages/d0/27/c621238d9995de1411b08917e2d1eed44b81be0616eb82c070bffa0edc9f/rc_foundry-0.1.5-py3-none-any.whl (545 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 545.2/545.2 kB 4.8 MB/s 0:00:00 Downloading https://pypi.tuna.tsinghua.edu.cn/packages/4b/51/7885547733e3191b82d7d245fa9f9d2d46ae44753215ab5172801fa72248/rc_foundry-0.1.4-py3-none-any.whl (545 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 545.4/545.4 kB 848.1 kB/s 0:00:00 Downloading https://pypi.tuna.tsinghua.edu.cn/packages/e4/59/1e08d10459949517fd6bfd07d694156e58c3caf7629dd26539486ab900a1/rc_foundry-0.1.3-py3-none-any.whl (545 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 545.4/545.4 kB 6.1 MB/s 0:00:00 Downloading https://pypi.tuna.tsinghua.edu.cn/packages/d9/fe/27efdc4a887136b710234bd2af79a5578d47558cd4127915717a1f94da7c/rc_foundry-0.1.2-py3-none-any.whl (545 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 545.4/545.4 kB 6.0 MB/s 0:00:00 Downloading https://pypi.tuna.tsinghua.edu.cn/packages/22/0f/8b26a779b38508f57a4e1f3df552773ae0d4a701d600ae8e96da3d2b4c82/rc_foundry-0.1.1-py3-none-any.whl (545 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 545.5/545.5 kB 2.1 MB/s 0:00:00 ERROR: Cannot install rc-foundry[all]==0.1.1, rc-foundry[all]==0.1.2, rc-foundry[all]==0.1.3, rc-foundry[all]==0.1.4, rc-foundry[all]==0.1.5, rc-foundry[all]==0.1.6 and rc-foundry[all]==0.1.7 because these package versions have conflicting dependencies. The conflict is caused by: rc-foundry[all] 0.1.7 depends on cuequivariance-ops-cu12>=0.6.1; sys_platform == "linux" and extra == "all" rc-foundry[all] 0.1.6 depends on cuequivariance-ops-cu12>=0.6.1; sys_platform == "linux" and extra == "all" rc-foundry[all] 0.1.5 depends on cuequivariance-ops-cu12>=0.6.1; sys_platform == "linux" and extra == "all" rc-foundry[all] 0.1.4 depends on cuequivariance-ops-cu12>=0.6.1; sys_platform == "linux" and extra == "all" rc-foundry[all] 0.1.3 depends on cuequivariance-ops-cu12>=0.6.1; sys_platform == "linux" and extra == "all" rc-foundry[all] 0.1.2 depends on cuequivariance-ops-cu12>=0.6.1; sys_platform == "linux" and extra == "all" rc-foundry[all] 0.1.1 depends on cuequivariance-ops-cu12>=0.6.1; sys_platform == "linux" and extra == "all" Additionally, some packages in these conflicts have no matching distributions available for your environment: cuequivariance-ops-cu12 To fix this you could try to:
- loosen the range of package versions you've specified
- remove package versions to allow pip to attempt to solve the dependency conflict
ERROR: ResolutionImpossible: for help visit https://pip.pypa.io/en/latest/topics/dependency-resolution/#dealing-with-dependency-conflicts In addition, I am an HPC user without sudo privileges, which makes it very difficult for me to build the SIF files needed to run Singularity on my own.
I don't understand why you install so many unnecessary packages and set many variables.
Simply using the following 3 commands is enough:
conda create -n fondry python=3.12 conda activate fondry pip install "rc-foundry[all]"HPC user can build a singlarity image. Once you got a def file, you can build it by yourself.
If you mean you cannot build sif in HPC, you may misunderstand how singularity works.
You need to build the sif on your local PC, then you can get a sif file, and copy it to HPC
In HPC, your script may include something like the following:
#!/bin/bash #PBS -N jobnane #PBS -l nodes=1:ppn=1 #PBS -q siais_gpu_5 #PBS -l walltime=80:00:00 #PBS -o log.out #PBS -e log.err module load cuda/7/12.2 module load apps/7/singularity/3.5.2 singularity run --nv \ -B cache:/cache \ -B workdir:/workdir \ image.sif \ # this sif file is built in your PC. script
I am aware that my .def file is far from perfect. Those packages and variables may not be necessary but at the same time I am not an expert in such kind of thing. Instead of dealing with figuring out dependencies one by one, I decided to keep whatever was working for my other apptainer containers and edit the .def file to install foundry. For me, it's faster to install this way then writing from scratch. Also, copying the config folder to that location was necessary to run rfd as it was looking for those files in container itself. (I created this container right after rfd3 was released).