BindCraft #37

tonykew · 2025-09-23T18:37:37Z

Bindcraft container image build docs with Slurm scripts and run examples

Note: currently only tested on x86_64 - will require further work for ARM64

Tony

Uncluear if this can be built on ARM64 - several files in the GitHub repo are x86_64 binaries: /app/functions/DAlphaBall.gcc /app/functions/FASPR /app/functions/dssp /app/functions/sc However, it may be possible to build then on ARM64 from GitHub sources: https://github.com/outpace-bio/DAlphaBall https://github.com/tommyhuangthu/FASPR https://github.com/cmbi/dssp https://github.com/cytokineking/sc-rs ??? Tony

Tony

naomeii · 2025-11-04T16:53:33Z

containers/2_ApplicationSpecific/BindCraft/README.md

+There are two sample .def files, FreeBindCraft.def and FreeBindCraft_with_PyRosetta.def
+The former does not install PyRosetta, the latter does.
+To build and use the PyRosetta version you must have a PyRosetta license.
+You must eaither complete the application for a non commercial license or purchase


Suggested change

You must eaither complete the application for a non commercial license or purchase

You must either complete the application for a non commercial license or purchase

naomeii · 2025-11-04T16:53:47Z

containers/2_ApplicationSpecific/BindCraft/README.md

+The former does not install PyRosetta, the latter does.
+To build and use the PyRosetta version you must have a PyRosetta license.
+You must eaither complete the application for a non commercial license or purchase
+a commercial licenses - see [PyRosetta Licensing](https://els2.comotion.uw.edu/product/pyrosetta) for more info.


Suggested change

a commercial licenses - see [PyRosetta Licensing](https://els2.comotion.uw.edu/product/pyrosetta) for more info.

a commercial license - see [PyRosetta Licensing](https://els2.comotion.uw.edu/product/pyrosetta) for more info.

naomeii · 2025-11-05T17:32:50Z

containers/2_ApplicationSpecific/BindCraft/README.md

+>   --interactive         Force interactive mode to collect target settings and options
+> ```
+
+See the [EXAMPLE file](./EXAMPLE.md) for more info.


Suggested change

See the [EXAMPLE file](./EXAMPLE.md) for more info.

See the [EXAMPLE file](./EXAMPLES.md) for more info.

naomeii · 2025-11-20T00:25:37Z

containers/2_ApplicationSpecific/BindCraft/EXAMPLES.md

+> ```
+-rw-rw-r-- 1 [CCRusername] nogroup 74686 Sep  9 15:39 /work/input/PDL1.pdb
+> ```


Suggested change

> ```

-rw-rw-r-- 1 [CCRusername] nogroup 74686 Sep 9 15:39 /work/input/PDL1.pdb

> ```

> ```

> -rw-rw-r-- 1 [CCRusername] nogroup 74686 Sep 9 15:39 /work/input/PDL1.pdb

> ```

naomeii · 2025-11-20T00:32:21Z

containers/2_ApplicationSpecific/BindCraft/EXAMPLES.md

+NOTE: BindCraft only uses one GPU (however, see [Using Multiple GPUs](#using-multiple-gpus) for work
+rounds with a Slurm job)
+
+For this example, the runtime is set to eigth hours, however such a run


Suggested change

For this example, the runtime is set to eigth hours, however such a run

For this example, the runtime is set to eight hours, however such a run

naomeii · 2025-11-20T06:05:41Z

containers/2_ApplicationSpecific/BindCraft/SLURM_EXAMPLE_WITH_PYROSETT.md

+cat slurm-21507614.out
+```
+
+sample output:


Suggested change

sample output:

Sample output:

naomeii · 2025-11-24T16:00:00Z

containers/2_ApplicationSpecific/BindCraft/README.md

+ --mem=0 --exclusive --time=01:00:00
+```
+
+sample outout:


Suggested change

sample outout:

Sample output:

naomeii · 2025-11-24T16:02:13Z

containers/2_ApplicationSpecific/BindCraft/SLURM_EXAMPLE_WITH_PYROSETT.md

+sacct --format="Elapsed" -j 21507614
+```
+
+Job 21507614 tuntime info:


Suggested change

Job 21507614 tuntime info:

Job 21507614 runtime info:

naomeii · 2025-11-24T16:04:42Z

containers/2_ApplicationSpecific/README.md

 |--------------------------------------|------------------------|
 | [Abaqus](./abaqus)                   | Guide to running Abaqus with Apptainer via Slurm batch script, command line, GUI access, and GPU support |
+| [AlphaFold 3](./AlphaFold-3)         | AlphaFold 3 container with steps for building and running a Data Pipeline and Inference via Apptainer and Slurm |
+| [BindCraft](./BindCraft)             | Free BindCraft container with steps for building and running with or withouth PyRosetta via Apptainer and Slurm |


Suggested change

| [BindCraft](./BindCraft) | Free BindCraft container with steps for building and running with or withouth PyRosetta via Apptainer and Slurm |

| [BindCraft](./BindCraft) | Free BindCraft container with steps for building and running with or without PyRosetta via Apptainer and Slurm |

naomeii · 2025-11-24T16:09:25Z

containers/2_ApplicationSpecific/BindCraft/SLURM_EXAMPLE.md

+
+> ```
+Running BindCraft on compute node: cpn-q09-20
+GPU info:
+GPU 0: Tesla V100-PCIE-32GB (UUID: GPU-54282c05-37f5-ccab-1be0-20bfd411efdd)
+[...]
+Stage 1: Test Logits
+1 models [0] recycles 1 hard 0 soft 0.02 temp 1 loss 14.04 helix 2.08 pae 0.86 i_pae 0.88 con 4.90 i_con 4.19 plddt 0.30 ptm 0.48 i_ptm 0.10 rg 16.75
+2 models [3] recycles 1 hard 0 soft 0.04 temp 1 loss 11.30 helix 0.97 pae 0.75 i_pae 0.79 con 4.18 i_con 4.01 plddt 0.43 ptm 0.49 i_ptm 0.11 rg 9.76
+[...]
+70 models [4] recycles 1 hard 0 soft 0.80 temp 1 loss 5.04 helix 1.57 pae 0.32 i_pae 0.30 con 2.38 i_con 2.86 plddt 0.73 ptm 0.66 i_ptm 0.49 rg 0.22
+71 models [0] recycles 1 hard 0 soft 0.84 temp 1 loss 5.49 helix 1.54 pae 0.37 i_pae 0.45 con 2.35 i_con 3.27 plddt 0.73 ptm 0.58 i_ptm 0.31 rg 0.26
+slurmstepd: error: *** JOB 21435656 ON cpn-q09-20 CANCELLED AT 2025-09-12T14:16:49 DUE TO TIME LIMIT ***
+> ```
+


Suggested change

> ```

Running BindCraft on compute node: cpn-q09-20

GPU info:

GPU 0: Tesla V100-PCIE-32GB (UUID: GPU-54282c05-37f5-ccab-1be0-20bfd411efdd)

[...]

Stage 1: Test Logits

1 models [0] recycles 1 hard 0 soft 0.02 temp 1 loss 14.04 helix 2.08 pae 0.86 i_pae 0.88 con 4.90 i_con 4.19 plddt 0.30 ptm 0.48 i_ptm 0.10 rg 16.75

2 models [3] recycles 1 hard 0 soft 0.04 temp 1 loss 11.30 helix 0.97 pae 0.75 i_pae 0.79 con 4.18 i_con 4.01 plddt 0.43 ptm 0.49 i_ptm 0.11 rg 9.76

[...]

70 models [4] recycles 1 hard 0 soft 0.80 temp 1 loss 5.04 helix 1.57 pae 0.32 i_pae 0.30 con 2.38 i_con 2.86 plddt 0.73 ptm 0.66 i_ptm 0.49 rg 0.22

71 models [0] recycles 1 hard 0 soft 0.84 temp 1 loss 5.49 helix 1.54 pae 0.37 i_pae 0.45 con 2.35 i_con 3.27 plddt 0.73 ptm 0.58 i_ptm 0.31 rg 0.26

slurmstepd: error: *** JOB 21435656 ON cpn-q09-20 CANCELLED AT 2025-09-12T14:16:49 DUE TO TIME LIMIT ***

> ```

> ```

> Running BindCraft on compute node: cpn-q09-20

> GPU info:

> GPU 0: Tesla V100-PCIE-32GB (UUID: GPU-54282c05-37f5-ccab-1be0-20bfd411efdd)

> [...]

> Stage 1: Test Logits

> 1 models [0] recycles 1 hard 0 soft 0.02 temp 1 loss 14.04 helix 2.08 pae 0.86 i_pae 0.88 con 4.90 i_con 4.19 plddt 0.30 ptm 0.48 i_ptm 0.10 rg 16.75

> 2 models [3] recycles 1 hard 0 soft 0.04 temp 1 loss 11.30 helix 0.97 pae 0.75 i_pae 0.79 con 4.18 i_con 4.01 plddt 0.43 ptm 0.49 i_ptm 0.11 rg 9.76

> [...]

> 70 models [4] recycles 1 hard 0 soft 0.80 temp 1 loss 5.04 helix 1.57 pae 0.32 i_pae 0.30 con 2.38 i_con 2.86 plddt 0.73 ptm 0.66 i_ptm 0.49 rg 0.22

> 71 models [0] recycles 1 hard 0 soft 0.84 temp 1 loss 5.49 helix 1.54 pae 0.37 i_pae 0.45 con 2.35 i_con 3.27 plddt 0.73 ptm 0.58 i_ptm 0.31 rg 0.26

> slurmstepd: error: *** JOB 21435656 ON cpn-q09-20 CANCELLED AT 2025-09-12T14:16:49 DUE TO TIME LIMIT ***

> ```

naomeii

Examples work, just correcting typos

tonykew added 5 commits September 23, 2025 14:32

Merge branch 'main' into BindCraft

8971067

Pagination fix

ca75d87

Tony

Merge branch 'main' into BindCraft

fdbe4dd

Added BindCraft to the containers "menu" README.md

2ff250c

Tony

naomeii suggested changes Nov 24, 2025

View reviewed changes

Merge branch 'main' into BindCraft

8237cbb

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Uh oh!

BindCraft #37

BindCraft #37

Uh oh!

tonykew commented Sep 23, 2025

Uh oh!

naomeii Nov 4, 2025

Uh oh!

naomeii Nov 4, 2025

Uh oh!

naomeii Nov 5, 2025

Uh oh!

naomeii Nov 20, 2025

Uh oh!

naomeii Nov 20, 2025

Uh oh!

naomeii Nov 20, 2025

Uh oh!

naomeii Nov 24, 2025

Uh oh!

naomeii Nov 24, 2025

Uh oh!

naomeii Nov 24, 2025

Uh oh!

naomeii Nov 24, 2025

Uh oh!

naomeii left a comment

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

2 participants

	You must eaither complete the application for a non commercial license or purchase
	You must either complete the application for a non commercial license or purchase

	a commercial licenses - see [PyRosetta Licensing](https://els2.comotion.uw.edu/product/pyrosetta) for more info.
	a commercial license - see [PyRosetta Licensing](https://els2.comotion.uw.edu/product/pyrosetta) for more info.

	See the [EXAMPLE file](./EXAMPLE.md) for more info.
	See the [EXAMPLE file](./EXAMPLES.md) for more info.

	For this example, the runtime is set to eigth hours, however such a run
	For this example, the runtime is set to eight hours, however such a run

	\| [BindCraft](./BindCraft) \| Free BindCraft container with steps for building and running with or withouth PyRosetta via Apptainer and Slurm \|
	\| [BindCraft](./BindCraft) \| Free BindCraft container with steps for building and running with or without PyRosetta via Apptainer and Slurm \|

BindCraft #37

Are you sure you want to change the base?

BindCraft #37

Uh oh!

Conversation

tonykew commented Sep 23, 2025

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

naomeii left a comment

Choose a reason for hiding this comment

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

2 participants