What to do with the note : The following floating-point exceptions are signalling: IEEE_DENORMAL?

HADDOCK
1

Hello!
This may be a real beginner issue, but I haven’t find the solution in this forum so far.

So here’s my problem :

I’m using a batch/queuing system (slurm) to run haddock2.4. Everything is fine when I call haddock2.4 to create the runX directory and the run.cns file. Once I confirmed that the run.cns files and directories name look ok and modified the queue parameters for :

{===>} queue_1=“sbatch”;
{===>} cns_exe_1="/project/chlandry/prg/haddock/2.4-2022-01/cns_solve_1.3/intel-x86_64bit-linux/bin/cns";
{===>} cpunumber_1= 8;

.I try to call haddock2.4 for the second time from the runX directory to start the docking. And I get this :

Starting HADDOCK on: 2022-05-21 14:09:46

HADDOCK version: 2.4 - January release
Python version: 2.7.18 (default, Mar 04 2021, 23:25:57) [GCC]
parsing run.cns file
parsing run.param in /project/chlandry/users/palem147/haddock/run1/data
reading parameters from the file /project/chlandry/users/palem147/haddock/run1/data/run.param
setting some variables:
N_COMP set to: 2
RUN_NUMBER set to: 1
HADDOCK_DIR set to: /project/chlandry/prg/haddock/2.4-2022-01/haddock2.4-2022-01
PROT_SEGID_2 set to: B
PROT_SEGID_1 set to: A
PDB_FILE1 set to: ./sho1_alone.pdb
PDB_FILE2 set to: ./AF_pbs2.pdb
PROJECT_DIR set to: .
N_COMP 2
RUN_NUMBER 1
HADDOCK_DIR /project/chlandry/prg/haddock/2.4-2022-01/haddock2.4-2022-01
PROT_SEGID_2 B
PROT_SEGID_1 A
PDB_FILE1 ./sho1_alone.pdb
PDB_FILE2 ./AF_pbs2.pdb
PROJECT_DIR .
looking for existing files
There is a problem with the CNS executable defined in run.cns:

Note: The following floating-point exceptions are signalling: IEEE_DENORMAL

=> HADDOCK stopped
##############################################################################

So it seems there is a denormal numbers problem in the run.cns file even though I didn’t modify the file(because I just want to run haddock before changing any parameters). In the forums I consulted, most told that it was not a real issue and that it can be solved easily, but I am not an administrator of the server I use, so I can’t modify or update software on it (or maybe I just don’t know what I’m looking for). So I was wondering if there was an option to haddock2.4 to avoid this issue.
(I also modified the UseLongFileNames.py file to have useLongJobFileNames = 1)

Thank you!

2

This is a CNS executable problem

How was CNS compiled?

Can you start it manually, e.g. simply from the command line:

/project/chlandry/prg/haddock/2.4-2022-01/cns_solve_1.3/intel-x86_64bit-linux/bin/cns

Was it compiled with the code provided with haddock2.4 (check the cns1.3 directory in the haddock2.4 dir)

3

Thank you for the prompt answer!
The installation was done by the administrator of the server so I’m not sure how cns was compiled, but apparently I can’t run cns manually. The error I get is:

%SETFPEPS increase value of MXFPEPS2 and recompile
%SETFPEPS error encountered: Could not determine machine epsilon
(CNS is in mode: SET ABORT=NORMal END)
WARNING: program encountered a fatal error.
However, in interactive mode, program execution
will continue. Proceed at your own risk.
Program will stop immediately.
============================================================
Maximum dynamic memory allocation: 0 bytes
Maximum dynamic memory overhead: 0 bytes
Program started at: on
Program stopped at: 15:18:31 on 21-May-2022
CPU time used: 0.0180 seconds
============================================================
Note: The following floating-point exceptions are signalling: IEEE_DENORMAL

I just looked into this forum (CNS errors before/after recompilation - #23 by garima.tanwar) to try and solve the compilation of cns. I followed the instructions to compile cns again but I get the same error.

4

I have finally found the answer I was looking for a bit deeper in the forum,
thanks for the answer!

5

May-be post the solution here for others who might read this thread :slight_smile:

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