CNS Installation - Segmentation Fault

HADDOCK
1

Hello,

I am running into issues compiling CNS. I keep getting this error after following the guide:

 make install
Installation directory: /home/.../haddock2.5/software/cns_solve_1.3/intel-x86_64bit-linux
copying files in instlib directory intel-x86_64bit-linux to intel-x86_64bit-linux
0read.me
Makefile.header.1.ifort
Makefile.header.2.gfortran
Makefile.header.3.ifort_mp
Makefile.header.4.pgf95
Makefile.header.5.ifort_mp_profile
Makefile.header.6.ifort_mp_tcheck
Makefile.header.7.gfortran_mp
arch_env
machine_c.c
machine_f.f
Using Makefile template for compiler: gfortran
linking source files to intel-x86_64bit-linux/source
Segmentation fault
make: *** [Makefile:38: install] Error 139

System Information:

  Kernel: 5.15.167.4-microsoft-standard-WSL2 arch: x86_64 bits: 64
    compiler: gcc v: 11.2.0
  Desktop: N/A dm: N/A Distro: Ubuntu 24.04.2 LTS (Noble Numbat)
CPU:
  Info: 8-core model: 12th Gen Intel Core i5-1240P bits: 64 type: MT MCP
    arch: Alder Lake rev: 3 cache: L1: 640 KiB L2: 10 MiB L3: 12 MiB
  Speed (MHz): avg: 2112 min/max: N/A cores: 1: 2112 2: 2112 3: 2112 4: 2112
    5: 2112 6: 2112 7: 2112 8: 2112 9: 2112 10: 2112 11: 2112 12: 2112 13: 2112
    14: 2112 15: 2112 16: 2112 bogomips: 67584
  Flags: avx avx2 ht lm nx pae sse sse2 sse3 sse4_1 sse4_2 ssse3 vmx
Graphics:
  Device-1: Microsoft Basic Render Driver driver: dxgkrnl v: 2.0.3
    bus-ID: 4982:00:00.0 chip-ID: 1414:008e
  Display: wayland server: Microsoft Corporation X.org driver: dri: swrast
    gpu: dxgkrnl display-ID: :0 screens: 1
  Screen-1: 0 s-res: 1024x768 s-dpi: 96
  Monitor-1: XWAYLAND0 res: 1024x768 size: N/A
  API: EGL v: 1.5 platforms: device: 1 drv: swrast surfaceless: drv: swrast
    x11: drv: swrast inactive: gbm,wayland,device-0
  API: OpenGL v: 4.1 vendor: microsoft mesa v: 24.2.8-1ubuntu1~24.04.1
    glx-v: 1.4 direct-render: yes renderer: D3D12 (Intel UHD Graphics)
    device-ID: ffffffff:ffffffff
Drives:
  Local Storage: total: 1 TiB used: 4.9 GiB (0.5%)
  ID-1: /dev/sda model: Virtual Disk size: 388.4 MiB serial: N/A
  ID-2: /dev/sdb model: Virtual Disk size: 2 GiB serial: N/A
  ID-3: /dev/sdc model: Virtual Disk size: 1024 GiB serial: N/A
Partition:
  ID-1: / size: 1006.85 GiB used: 4.9 GiB (0.5%) fs: ext4 dev: /dev/sdc
Swap:
  ID-1: swap-1 type: partition size: 2 GiB used: 0 KiB (0.0%) priority: -2
    dev: /dev/sdb
Info:
  Memory: total: 8 GiB note: est. available: 7.61 GiB used: 720.8 MiB (9.2%)
  Processes: 34 Power: uptime: 9h 8m Init: systemd v: 255
    target: graphical (5) default: graphical
  Packages: pm: dpkg pkgs: 641 Compilers: gcc: 13.3.0 Shell: Bash v: 5.2.21
    running-in: Relay(54071) inxi: 3.3.34

Does anyone know what could be the cause? Or how to get around it?

Thanks!

2

Haddock3 can be installed by pip install haddock3 now and doesn’t need to compile CNS anymore.

For haddock2?

3

not the case for haddock2

But we do provide links to CNS executables in the email containing the instructions

4

Hello,
I’m trying to install haddock2.5. I followed the provided instructions on compiling the CNS executable.

5

Did you simply try to use a pre-compiled executable?

6

I have tried, but haven’t had much success with pre-compiled executables from other working haddock installs

7

Is there a way to use a pre-compiled executable but update the CNS_solve location variable?

8

haddock only needs the executable - it is defined in run.cns - nothing else

9

I recompiled a CNS executable I thought was working but now I see it does not fully compile while building an apptainer image:

making Makefile in source directory
making compiler-test directory in intel-x86_64bit-linux
testing Fortran and C compilers
compiling: gcc -O -DINTEGER='long int' -DCNS_ARCH_TYPE_LINUX 
C compiler passes test
compiling: gfortran -fdefault-integer-8 -w -fallow-argument-mismatch -O3  -funroll-loops -ffast-math -march=native -mtune=native  
linking: gfortran -w  -static-libgfortran
Fortran compiler passes test
making utility programs
make[2]: *** No rule to make target 'compile-utils'.  Stop.
make[1]: *** [Makefile:60: utils] Error 2
10

Our most up to date instructions for compiling CNS can be found at:

[

97be5584-db7b-4a0a-80d2-2aba6114567b.png
97be5584-db7b-4a0a-80d2-2aba6114567b.png1024×512 116 KB

haddock3/docs/CNS.md at main · haddocking/haddock3
github.com
](https://github.com/haddocking/haddock3/blob/main/docs/CNS.md)
11

Thank you, I have followed these instructions but I still can’t get past the Error 2.

12

Try the following:

go directly into the intel-x86_64bit-linux/source directory and type make cns_solve

Also best to use a rather recent version of gcc/gfortran (e.g. 13 or 14)