From f800847be0481f223265ce861d017f1d7b0a1126 Mon Sep 17 00:00:00 2001
From: Amirreza Aleyasin <98012508+Amirreza-0@users.noreply.github.com>
Date: Wed, 17 Jun 2026 22:58:52 +0200
Subject: [PATCH 1/2] Update torch version to include CUDA support

---
 pip_requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pip_requirements.txt b/pip_requirements.txt
index 397ef2031..5e677cad0 100644
--- a/pip_requirements.txt
+++ b/pip_requirements.txt
@@ -13,7 +13,7 @@ pdb2sql==0.5.3
 protobuf==3.20.1
 tabulate==0.9.0
 toolz==1.0.0
-torch==1.10.1
+torch==1.10.1+cu113
 typing-extensions==3.7.4.3
 urllib3==1.26.14
 python-Levenshtein

From 7225ad01d3026bf4a3fb45e61869a06e0eaa6ee0 Mon Sep 17 00:00:00 2001
From: Amirreza Aleyasin <98012508+Amirreza-0@users.noreply.github.com>
Date: Tue, 23 Jun 2026 10:32:07 +0200
Subject: [PATCH 2/2] Update dependencies in PMGen.yml

---
 PMGen.yml | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/PMGen.yml b/PMGen.yml
index 3a28ec060..eb4de3d20 100644
--- a/PMGen.yml
+++ b/PMGen.yml
@@ -30,9 +30,7 @@ dependencies:
   - click=8.1.8=pyh707e725_0
   - contextlib2=21.6.0=pyhd8ed1ab_1
   - cryptography=44.0.0=py39h7170ec2_0
-  - cuda-version=11.8=h70ddcb2_3
-  - cudatoolkit=11.8.0=h4ba93d1_13
-  - cudnn=8.9.7.29=hbc23b4c_3
+  - cudatoolkit=11.2
   - curl=7.88.1=hdc1c0ab_1
   - entrez-direct=22.4=he881be0_0
   - filelock=3.17.0=pyhd8ed1ab_0
@@ -85,7 +83,6 @@ dependencies:
   - libhwloc=2.9.1=hd6dc26d_0
   - libiconv=1.18=h4ce23a2_1
   - libidn2=2.3.7=hd590300_0
-  - libjpeg-turbo=2.1.5.1=hd590300_1
   - liblapack=3.9.0=16_linux64_mkl
   - liblzma=5.6.3=hb9d3cd8_1
   - liblzma-devel=5.6.3=hb9d3cd8_1
@@ -114,7 +111,6 @@ dependencies:
   - mpmath=1.3.0=pyhd8ed1ab_1
   - multidict=6.1.0=py39h9399b63_2
   - muscle=5.1=h4ac6f70_3
-  - nccl=2.24.3.1=h03a54cd_0
   - ncurses=6.5=h2d0b736_2
   - networkx=3.2=pyhd8ed1ab_0
   - numpy=1.22.4=py39hc58783e_0
@@ -156,7 +152,7 @@ dependencies:
   - python-dateutil=2.9.0.post0=pyhff2d567_1
   - python-tzdata=2025.1=pyhd8ed1ab_0
   - python_abi=3.9=5_cp39
-  - pytorch=2.5.*
+  - pytorch=2.0.0=cuda112py39ha9981d0_200
   - pytz=2024.1=pyhd8ed1ab_0
   - pyu2f=0.1.5=pyhd8ed1ab_1
   - pyyaml=6.0.2=py39h9399b63_2