CNS errors before/after recompilation

eiso · April 7, 2016, 8:34am

I recompiled CNS with the files provided in the HADDOCK2.2 distribution

I get the following error message:

cns < run1/protocols/generate_A.inp
%SETFPEPS increase value of MXFPEPS2 and recompile
%SETFPEPS error encountered: Could not determine machine epsilon
(CNS is in mode: SET ABORT=NORMal END)

ABORT mode will terminate program execution.

Program will stop immediately.

But if I adjust this param MXFPEPS2 in machvar.inc I get another error

cns_solve_1.3/intel-x86_64bit-linux/bin/cns < run1/protocols/generate_A.inp
%SETFPEPS Machine epsilon determined to be 0.494-323
%SETFPEPS error encountered: Machine epsilon value is too small
(CNS is in mode: SET ABORT=NORMal END)

What am I doing wrong?

Eiso

amjjbonvin · April 7, 2016, 9:02am

Googling this error message you can find a number of possible solutions/causes.
It seems to be related to 32/64 bits and depending on the compiler you are using.

Various solutions have been proposed:

Removing -fast-math as a compiler option
Modify the machvar.f like this (line numbers on the left). The file should in the source folder
65 ONEP = DPTRUNC(ONE) + DPTRUNC(FPEPS) 66 ONEM = DPTRUNC(ONE) - DPTRUNC(FPEPS) 67 IF (ONE .EQ. ONEP .OR. ONE .EQ. ONEM) THEN 68 I = I - 1
Let us know what works for you and also which compiler/OS combination your are using

eiso · April 7, 2016, 1:43pm

those lines were already in the code.

I’m using Centos-7 + gfortran
%fortran --version
GNU Fortran (GCC) 4.9.2

I’ll try to remove the flag…

E

eiso · April 13, 2016, 10:49am

removing the -ffast-math gets rid of the %SETFPEPS error but
creates a new one.

cns_solve_1.3/intel-x86_64bit-linux/bin/cns < run1/protocols/generate_A.inp

[…snip…]
RTFRDR>! DNA-RNA-ALLATOM.TOP
RTFRDR>
RTFRDR>set message ? end eval ($old_message=$result) set echo ? end eval ($old_echo=$result)
MESSage=NORM
EVALUATE: symbol $OLD_MESSAGE set to “NORM” (string)
ECHO=TRUE {ON}
EVALUATE: symbol $OLD_ECHO set to TRUE (logical)
RTFRDR>set message=off echo=off end
%AUTOAN error encountered: exceeded MXRTP (RTF) parameter --> recompile program
(CNS is in mode: SET ABORT=NORMal END)

ABORT mode will terminate program execution.

Program will stop immediately.

I will try adjusting MXRTP but I’m a bit surprised. The system is not very large
(170aa)

Eiso

amjjbonvin · April 13, 2016, 1:30pm

Indeed - we run into that too. Probably coming from reading several parameter files in the script

eiso · April 13, 2016, 2:52pm

could be due to the ACPYPE topologies, they have more dihedrals than
usual prodrg topologies.

You could distribute the cns source files with adjusted params right?
Or is it unusual that this is a problem?

I set MXRTP to 4000 and now there’s not error.
Do you expect a performance hit from leaving the -ffast-math out?

E

Eiso

amjjbonvin · April 15, 2016, 11:30am

indeed - will make a note of this.

srinivas_penumutchu · August 10, 2016, 8:36pm

Dear Eiso,

if you fixed the problem, could you please let me know more in detail that how you fix same error as follows ?. how to remove the -fast-math as a compiler option ?.
Because i am getting same error. I am trying to compile with gcc and gfortan !
%SETFPEPS Machine epsilon determined to be 0.494-323
%SETFPEPS error encountered: Machine epsilon value is too small
(CNS is in mode: SET ABORT=NORMal END)

Thanking you !

I am using OS X EI Captain
version 10.11.3
Mac Pro (Early 2009)

srinivas_penumutchu · August 10, 2016, 9:33pm

Dear Dr. Alexandre Bonvin,

could you please let me know that how to issue the command for Removing -fast-math as a compiler option ?. Because i am getting following error. while cns installation.

%SETFPEPS Machine epsilon determined to be 0.494-323
%SETFPEPS error encountered: Machine epsilon value is too small

Thanking you !

eiso · August 10, 2016, 11:01pm

this worked for me

I set MXRTP to 4000 and now there’s no error

E

Srinivas Penumutchu wrote:

amjjbonvin · August 11, 2016, 7:03am

simply edit the Makefile you are using and remove that option

srinivas_penumutchu · August 11, 2016, 2:49pm

Dear Eiso,

Where did you edit the MXRTP ?. Could you please let me know file name and location ?

Thanking you !

amjjbonvin · August 11, 2016, 3:00pm

in rtf.inc in the source directory

srinivas_penumutchu · August 11, 2016, 4:01pm

Thanks you Dr. Alexandre Bonvin, , finally it is working after i did four modifications ! I hope it will be helpful to someone

first modification
set MXFPEPS2 value to 8192 in machvar.inc

second modification
removed flag -fastm in make file

third modification
MXRTP to 4000 in rtf.inc in the source directory

fourth modification

add the below line in the machvar.f
WRITE (6,’(I6,E10.3,E10.3)’) I, ONEP, ONEM
just above line 67, which looks like this:
IF (ONE .EQ. ONEP .OR. ONE .EQ. ONEM) THEN

joaor · August 16, 2016, 5:29am

These are two unrelated errors:

What @eiso was dealing with is a problem of the number of parameters and the ‘dynamic’ memory allocation of CNS.

What @srinivas_penumutchu found happens quite often in Mac OSX and for some reason is only solved with the solution you posted, which just adds a print statement… This will add a bunch of unnecessary output to the CNS initialization headers though… Would be great if someone with more FORTRAN skills could take a look at it!

bosmith · June 2, 2017, 2:04pm

Suggestion for a proper solution to this problem:

Replace the SETFPEPS subroutine as follows

C ==========================================================================
C
SUBROUTINE SETFPEPS
C
IMPLICIT NONE
C I/O
INCLUDE ‘numbers.inc’
INCLUDE ‘machvar.inc’
C
C Determine the machine epsilon i.e. the smallest FPEPS such that both
C 1+FPEPS and 1-FPEPS are different from 1.
C
C local
DOUBLE PRECISION ONEDP
DOUBLE COMPLEX DBCOMP
C
C external
C NONE
C
C begin
C
C ONEDP doesn’t really need to be defined - EPSILON() only needs to know
C the type
ONEDP=(1.00)
FPEPS = EPSILON(ONEDP)
DBCOMP = DCMPLX(ZERO,ZERO)
CALL DECLAR(‘FP_EPSILON’, ‘DP’, ’ ', DBCOMP, FPEPS)
RETURN
END

amjjbonvin · June 4, 2017, 7:10pm

Thanks Brian - is this generic for any OS? Or OSX-specific?

bosmith · June 5, 2017, 8:56am

Hi Alexandre,

This should be a generic solution. I see the issue on LINUX (CentOS 7) with gcc 4.8.5.

Brian

garima.tanwar · December 15, 2017, 11:12am

Hi Srinivas sir,
Can you please explain how to remove flag -fastm in the makefile?

garima.tanwar · December 15, 2017, 11:20am

After replacing subrotines in machvar.f file
and then recompile cns_solve
shows error:

make[3]: Target '../bin/cns_solve' not remade because of errors.
Makefile:58: recipe for target 'cns_solve' failed
make[2]: *** [cns_solve] Error 2
Makefile:64: recipe for target 'cns_solve' failed
make[1]: *** [cns_solve] Error 2

Topic		Replies	Views
CNS executable not working HADDOCK	4	18	November 22, 2024
Error during rigid body stage of docking HADDOCK	2	1048	December 21, 2017
Error in the simulated annealing stage of protein-protein docking HADDOCK	5	625	April 13, 2022
%XXNXTFI-ERR: invalid or unknown path-name: "RUN" HADDOCK	6	450	June 2, 2021
Haddock examples in ./examples are failing on topology creation HADDOCK	4	364	February 24, 2022

CNS errors before/after recompilation

Related topics