CP2K-2025.2 Apptainer(singularity) 镜像分享

s8ga

1. 前言
  站内的 CP2K Singularity 镜像都比较老了，最近需要频繁的更换计算节点，所以编译了一份带 全部依赖的CP2K 容器镜像，方便在不同服务器上使用。
  使用了 podman构建CP2K 然后使用 apptainer(singularity 的开源版本)打包 sif
1.1 使用环境要求

• 单机：
  不需要root、需要足够高的内核版本 (3.8+)
  无法在docker内嵌套运行 （可以在 wsl / kvm / vmware 等虚拟化方案内运行）
• 集群：
  没尝试过
  

1.2 镜像列表
  文件下载链接: https://pan.baidu.com/s/1AdlUGY40yEmDj-M32Q37Xw?pwd=s8ga

• cp2k-opensource-2025.2 (260501添加) (regtest 通过)
  标准 2025.2 build
  
• cp2k-opensource-2025.2-force-avx512 (260501添加) (regtest 通过)
  解决了使用 avx2处理器 上构建的 cp2k在  avx512处理器 上使用时
  Setting real_kernel for ELPA failed 的问题 (强制编译 ELPA的 AVX512内核就好了)
  
• cp2k-rocm-2026.1-gfx942 (260501添加) (实验性)
  AMD Mi300X 加速版本 (未经充分测试)
  
• cp2k-mkl-2025.2-experimental (260501添加) (regtest 通过) (实验性)
  使用的是Openmpi + mkl 构建方式
  存在经验性修补内容，不推荐在生产环境中使用
  与Opensource速度基本相同
  

1.3 下个release

• cp2k master branch (当有重大更新的时候)
• cp2k 2026.2
  

2.使用指南

• 先将 镜像 下载好，并将你选择的 sif文件 和 apptainer-1.4.5-3.el8-x86_64.run放入服务器你选择的位置
• 1. # 1.首先切换到你放置文件的目录
     
  2. cd "Your preferred location"
     
  3. 
     
  4. # 2.给run文件添加可执行权限
     
  5. chmod +x apptainer-1.4.5-3.el8-x86_64.run
     
  6. 
     
  7. # 3.解压apptainer
     
  8. ./apptainer-1.4.5-3.el8-x86_64.run
     
  9. 
     
  10. # 4.将apptainer source到PATH中
      
  11. # 请根据屏幕上面的提示 source指定文件
      
  12. # (仅供参考) source /tmp/apptainer-test/apptainer-bundle/activate-apptainer.sh
      
  13. 
      
  14. # 5.你可以使用 apptainer run 来启动镜像 (下面的例子仅供参考 - 只是显示了cp2k的版本号/编译信息)
      
  15. apptainer run cp2k-opensource_2025.2-force-avx512.sif mpirun cp2k.psmp --version | head -n10
      
  16. # 或者是使用screen + apptainer shell 方式启动
      
  17. screen apptainer shell cp2k-opensource_2025.2-force-avx512.sif
      
  18. 
      
  19. # 具体使用方式
      
  20. # apptainer exec cp2k-opensource_2025.2-force-avx512.sif mpirun -np <Input thread count> cp2k.psmp -i [Your Input].inp -o [Your Output].out
      
  21. # 或者是使用screen + apptainer shell 方式启动
      
  22. apptainer shell cp2k-opensource_2025.2-force-avx512.sif
      
  23. # <在新的shell内部>
      
  24. mpirun -np <Input thread count> cp2k.psmp -i [Your Input].inp -o [Your Output].out
      
  25. 
      
  26. ######################################
      
  27. 
      
  28. # 6.如果你想运行cp2k的regtest
      
  29. apptainer shell cp2k-opensource_2025.2-force-avx512.sif
      
  30. # 然后在容器内部运行
      
  31. python /opt/cp2k/tests/do_regtest.py  --mpiranks 2 --ompthreads 2 --maxtasks $(nproc) --keepalive --workbasedir /tmp --mpiexec "mpirun $MPI_RUNVAR -np {N}" $(dirname $(which cp2k.psmp)) psmp

  复制代码
• 如果用户重新登录了，只要找到 4提示的sh文件位置，source后正常使用
  如果你想看更形象一点的使用demo的话，可以查看这个 Demo
  

3. 构建镜像
(更详细的信息 请参照 构建程序链接)
(构建过程所有文件已经开源)

构建机要求：
需要有podman, uv，同时需要有良好的网络连接
推荐使用 Debian / WSL2 或 VMWare 进行编译

1. 前置条件
   
2. # 0. cd 到 clone下来的目录
   
3. # cd HPC-Container-Factory
   
4. 
   
5. # 1. Python 依赖
   
6. uv venv venv
   
7. uv pip install -r requirements.txt --python ./venv/bin/python
   
8. 
   
9. # 2. 需要 Podman
   
10. podman info
    
11. 
    
12. # 3. 需要 clone spack
    
13. # 下载 Spack v1.1.0 release tarball
    
14. mkdir -p assets
    
15. curl -fSL -o assets/spack-v1.1.0.tar.gz \
    
16.   https://github.com/spack/spack/releases/download/v1.1.0/spack-1.1.0.tar.gz
    
17. 
    
18. # 解压出 spack-src/（bootstrap 阶段需要）
    
19. tar -xzf assets/spack-v1.1.0.tar.gz -C assets/
    
20. mv assets/spack-1.1.0 assets/spack-src
    
21. 
    
22. # 4. 激活环境
    
23. source ./activate.sh
    
24. 
    
25. # 5. 准备离线资源 (spack 源代码包)
    
26. python generate.py assets --env cp2k-opensource-2025.2-force-avx512
    
27. # 预计输出
    
28. # [OK]    All packages available in mirror
    
29. 
    
30. # 6. 构建
    
31. python generate.py build --app-version cp2k-opensource-2025.2-force-avx512 --network-host
    
32. # 构建过程较慢 大概需要45 min +
    
33. # 预计输出
    
34. # Successfully tagged localhost/cp2k-opensource:2025.2-force-avx512
    
35. 
    
36. # 7. 转换为 SIF文件
    
37. python generate.py build-sif --app-version  cp2k-opensource-2025.2-force-avx512
    
38. # 首次使用需要安装apptainer (需要一些时间)
    
39. # 产出文件在 artifacts
    
40. 
    
41. # 8. 运行
    
42. source ./activate.sh
    
43. apptainer shelll artifacts/cp2k-opensource_2025.2-force-avx512.sif
    
44. 
    
45. # 9. [可选] 打包apptainer 便于分发至其他机器
    
46. python generate.py pack-apptainer
    
47. # 产物在 artifact/apptainer-<version>-x86_64.run

复制代码

如果有需要的话，构建产物可以随意分享（MIT协议）

Happy Computing!

牧生

我跑一个任务，报MPI的问题，但我无法解决。
此外，不知道为何，我的9950X3D，架构被自动认作intel的Haswell


第一个
apptainer exec cp2k-mkl_2025.2-experimental.sif mpirun -np 1 cp2k.psmp -i OPT.inp -o OPT.out
SIRIUS 7.9.0, git hash: https://api.github.com/repos/ele ... git/ref/tags/v7.9.0
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
  Proc: [[5169,1],0]
  Errorcode: 1

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
prterun has exited due to process rank 0 with PID 0 on node jing calling
"abort". This may have caused other processes in the application to be
terminated by signals sent by prterun (as reported here).
--------------------------------------------------------------------------




第二个

apptainer exec cp2k-rocm_2026.1-gfx942.sif mpirun -np 6 cp2k.psmp -i OPT.inp -o OPT.out
Core not found: ZEN4
Core: Haswell
Core not found: ZEN4
Core: Haswell
Core not found: ZEN4
Core: Haswell
Core not found: ZEN4
Core: Haswell
Core not found: ZEN4
Core: Haswell
Core not found: ZEN4
Core: Haswell
Inconsistency in warp sizes: Cuda/Hip indicates warp size = 64, while the gpu_properties files indicates warp_size = 32.
Inconsistency in warp sizes: Cuda/Hip indicates warp size = 64, while the gpu_properties files indicates warp_size = 32.
Inconsistency in warp sizes: Cuda/Hip indicates warp size = 64, while the gpu_properties files indicates warp_size = 32.
Inconsistency in warp sizes: Cuda/Hip indicates warp size = 64, while the gpu_properties files indicates warp_size = 32.
Inconsistency in warp sizes: Cuda/Hip indicates warp size = 64, while the gpu_properties files indicates warp_size = 32.
Inconsistency in warp sizes: Cuda/Hip indicates warp size = 64, while the gpu_properties files indicates warp_size = 32.
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
  Proc: [[46349,1],0]
  Errorcode: 1

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
prterun has exited due to process rank 0 with PID 0 on node jing calling
"abort". This may have caused other processes in the application to be
terminated by signals sent by prterun (as reported here).
--------------------------------------------------------------------------



第三个apptainer exec cp2k-opensource_2025.2-force-avx512.sif mpirun -np 6 cp2k.psmp -i OPT.inp -o OPT.out
Core not found: ZEN4
Core: Haswell
Core not found: ZEN4
Core: Haswell
Core not found: ZEN4
Core: Haswell
Core not found: ZEN4
Core: Haswell
Core not found: ZEN4
Core: Haswell
Core not found: ZEN4
Core: Haswell
SIRIUS 7.9.0, git hash: https://api.github.com/repos/ele ... git/ref/tags/v7.9.0
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
  Proc: [[33067,1],0]
  Errorcode: 1

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
prterun has exited due to process rank 0 with PID 0 on node jing calling
"abort". This may have caused other processes in the application to be
terminated by signals sent by prterun (as reported here).
--------------------------------------------------------------------------