Structure fail / error - CPU number

Giorgos_F · February 26, 2024, 11:31am

Hello everyone,

A) I would like your help with the following issue:

I am running HADDOCK2.4 locally. The goal is to perform docking of a peptide to a protein binding site. Recently, I changed the following parameters in the CNS file as shown below:

{===>} em_it0=false;
{===>} em_it1=false;
{===>} em_itw=false;
{===>} hbond_firstit=0;
{===>} initiosteps=2000;
{===>} cool1_steps=2000;
{===>} cool2_steps=4000;
{===>} cool3_steps=4000;

These changes though lead to the peptides failing to dock and with the log file in the run1 folder mentioning the following line:
“Iteration 1 structure 1: Performing only EM …”

The output of the error is the following:

Timeout - deleting:  /media/.../run1/bdsite_1_haddock_pep_run1_it1_refine_1.out
Time-out of structure 1
Waiting to restart job...
------------------------------------------------------------
Structure    1: crashed
Structure    2: running
Structure    3: running
Structure    4: running
Structure    5: running
------------------------------------------------------------

    calculating structure 1
Traceback (most recent call last):
  File "/media/.../haddock_software/haddock2.4-2023-08/Haddock/RunHaddock.py", line 655, in <module>
    run['haddock_dir'], run)
  File "/media/.../haddock_software/haddock2.4-2023-08/Haddock/Main/MHaddock.py", line 590, in ForAllIterations
    open(stdoutFN, 'w')
IOError: [Errno 2] No such file or directory: '/media/.../run1/bdsite_1_haddock_pep_run1_it1_refine_1.out'

In the strctures/it1 folder the first file has the extension “fail” in its name (“filename.fail”).

Docking was run again with the em_it (em_it0, em_it1, em_itw) parameters set equal to true but again the same error occurred.

I would also like to add that no “out.gz” file was created for the corresponding failed file. The “out.gz” file of the subsequent structure (after the failed one) contained the “pep_…_t1_refine_2.out” file which contained the following lines at the end of it:

 NOEPRI: RMS diff. =   1.027,  #(violat.> 0.3)=    10 of     14 NOEs
 NOEPRI: RMS diff. class AMBI =   1.027,  #(viol.> 0.3)=    10 of     14 NOEs
 --------------- cycle=    48 --------------------------------------------------
 | Etotal =2.458      grad(E)=0.513      E(BOND)=0.000      E(ANGL)=0.000      |
 | E(DIHE)=0.000      E(IMPR)=0.000      E(VDW )=-46.454    E(ELEC)=-13.630    |
 | E(HARM)=0.000      E(CDIH)=0.000      E(NOE )=62.541                        |
 -------------------------------------------------------------------------------
 Total number of dihedral angle restraints=     0
  overall scale =  200.0000
 Number of dihedral angle restraints=    0
 Number of violations greater than    5.000:     0
 RMS deviation=   0.000
 (atom-i        |atom-j        )    dist.   equil.   delta    energy   const. 

 (atom-i        |atom-j        )    dist.   equil.   delta    energy   const. 

 (atom-i        |atom-j        )    dist.   equil.   delta    energy   const. 

 (atom-i        |atom-j        )    dist.   equil.   delta    energy   const. 

 (atom-i        |atom-j        )    dist.   equil.   delta    energy   const. 

 (atom-i        |atom-j        )    dist.   equil.   delta    energy   const. 

 (atom-i        |atom-j        )    dist.   equil.   delta    energy   const. 

 Number of violations greater    0.050:     0
 (atom-i        |atom-j        |atom-k        )  angle    equil.     delta    energy  const. 

 (atom-i        |atom-j        |atom-k        )  angle    equil.     delta    energy  const. 

 (atom-i        |atom-j        |atom-k        )  angle    equil.     delta    energy  const. 

 (atom-i        |atom-j        |atom-k        )  angle    equil.     delta    energy  const. 

 (atom-i        |atom-j        |atom-k        )  angle    equil.     delta    energy  const. 

 (atom-i        |atom-j        |atom-k        )  angle    equil.     delta    energy  const. 

 (atom-i        |atom-j        |atom-k        )  angle    equil.     delta    energy  const. 

 Number of violations greater    5.000:     0
 (atom-i        |atom-j        |atom-k        |atom-L        )    angle    equil.   delta    energy   const.   period

 (atom-i        |atom-j        |atom-k        |atom-L        )    angle    equil.   delta    energy   const.   period

 (atom-i        |atom-j        |atom-k        |atom-L        )    angle    equil.   delta    energy   const.   period

 (atom-i        |atom-j        |atom-k        |atom-L        )    angle    equil.   delta    energy   const.   period

 (atom-i        |atom-j        |atom-k        |atom-L        )    angle    equil.   delta    energy   const.   period

 (atom-i        |atom-j        |atom-k        |atom-L        )    angle    equil.   delta    energy   const.   period

 (atom-i        |atom-j        |atom-k        |atom-L        )    angle    equil.   delta    energy   const.   period

 Number of violations greater    5.000:     0
 (atom-i        |atom-j        |atom-k        |atom-L        )    angle    equil.   delta    energy   const.   period

 (atom-i        |atom-j        |atom-k        |atom-L        )    angle    equil.   delta    energy   const.   period

 (atom-i        |atom-j        |atom-k        |atom-L        )    angle    equil.   delta    energy   const.   period

 (atom-i        |atom-j        |atom-k        |atom-L        )    angle    equil.   delta    energy   const.   period

 (atom-i        |atom-j        |atom-k        |atom-L        )    angle    equil.   delta    energy   const.   period

 (atom-i        |atom-j        |atom-k        |atom-L        )    angle    equil.   delta    energy   const.   period

 (atom-i        |atom-j        |atom-k        |atom-L        )    angle    equil.   delta    energy   const.   period

 Number of violations greater   30.000:     0
 SURFAC: half the sigma value being used for atomic radii.
 SURFAC: ACCEssible surface area
 SURFAC: ACCUracy= 0.07 RH2O=  1.40
         Z-grid=  0.32 number-of-Z-sections=  179
         measures-of-arc= 25536 and 30386
 SURFAC: half the sigma value being used for atomic radii.
 SURFAC: ACCEssible surface area
 SURFAC: ACCUracy= 0.07 RH2O=  1.40
         Z-grid=  0.32 number-of-Z-sections=   48
         measures-of-arc=   226 and   485
 SURFAC: half the sigma value being used for atomic radii.
 SURFAC: ACCEssible surface area
 SURFAC: ACCUracy= 0.07 RH2O=  1.40
         Z-grid=  0.32 number-of-Z-sections=  179
         measures-of-arc= 26408 and 31257
 MOMENTS
 169345.45087849 -22771.38631221 -90072.12393123
                 180874.31867501  33013.50389845
                                 537834.76624541

 HEAP: maximum use      =  3001720376 current use      =     1536000 bytes
 HEAP: maximum overhead =        5776 current overhead =        1232 bytes
          ============================================================
           Maximum dynamic memory allocation:  3001720376 bytes
           Maximum dynamic memory overhead:          5776 bytes
           Program started at: 12:48:50 on 26-Feb-2024
           Program stopped at: 12:55:19 on 26-Feb-2024
           CPU time used:     387.5970 seconds
          ============================================================

Do you have any idea of why is this happening?

Furthermore, these parameters are under the section of:

"{========================== Cryo-EM parameters ============================}",

Therefore as long as we do not have structures from Cryo-EM, I suppose that these parameters should remain false correct?

B) I would also like your insight regarding the following matter:

I am using a server with a certain number of nodes that in total provide me with 32 or 48 CPUs. I am trying to make the most out of these CPUs by setting in the CNS file the following:

{===>} cpunumber_1=32;

Is there a better way to set the parameters in the CNS file in order for Haddock to utilize at greater length these CPUs (e.g., use “queue_2” and “cpunumber_2”)?

amjjbonvin · March 6, 2024, 2:35pm

Looking at the error below, I think you have a typo in your path.

Three dots must not be correct

Giorgos_F · March 6, 2024, 6:37pm

I had replaced a part of the path with the three dots just to make it smaller and easier to read for the error message. In more recent tries I have managed to avoid this error by using 16 CPUs and the following steps:

{===>} initiosteps=500;
{===>} cool1_steps=500;
{===>} cool2_steps=1000;
{===>} cool3_steps=1000;

Although still when increasing the steps (e.g., to 1000 1000 2000 2000 or 2000 2000 4000 4000) while the CPUs are 16 or 32 the error does occur again. It always seems to affect the first structure of it1 which fails and then docking is terminated.

amjjbonvin · March 7, 2024, 8:39am

Could be something bad happening to that model …

You could also try changing the random seed.

But I can not see how changing the number of CPUs would affect that.

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Structure fail / error - CPU number

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