[gmx-users] GROMACS 3.3.1 installation on SGI (Irix)

james zhang james.zhangj at gmail.com
Sun Jul 16 06:59:08 CEST 2006


Hi:

I have just fixed the following make_edi.c errors, by

changing the code to:

{ "-linfix", FALSE, etSTR, {&evSelections[evLINFIX]},
{ "-linacc", FALSE, etSTR, {&evSelections[evLINACC]},
{ "-radfix", FALSE, etREAL, {&evSelections[evRADFIX]},

And I succeeded to compile and install gromacs 3.3.1.

But I still can't run the mdrun program on the sgi irix machine.The
mdrun doesn't work.

Please help! Thanks a lot.

James

____________________________________________________________________________
cc-1028 cc: ERROR File = make_edi.c, Line = 579
  The expression used must have a constant value.

      { evStepOptions[evLINFIX], FALSE, etSTR, {&evParams[evLINFIX]},
        ^

cc-1028 cc: ERROR File = make_edi.c, Line = 581
  The expression used must have a constant value.

      { evStepOptions[evLINACC], FALSE, etSTR, {&evParams[evLINACC]},
        ^

cc-1028 cc: ERROR File = make_edi.c, Line = 583
  The expression used must have a constant value.

      { evStepOptions[evRADFIX], FALSE, etREAL, {&radfix},
        ^

cc-1552 cc: WARNING File = make_edi.c, Line = 622
  The variable "bTop" is set but never used.

      bool bTop, bM, bFit1;
           ^

3 errors detected in the compilation of "make_edi.c".
*** Error code 2 (bu21)
*** Error code 1 (bu21)
*** Error code 1 (bu21)
____________________________________________________________________________

I really appreciate your help.

Kind Regards
Akshay

Akshay Patny


Graduate Research Assistant
Faser Hall 417, Department of Medicinal Chemistry
Research Institute of Pharmaceutical Sciences
University of Mississippi
University, MS 38677
E-mail: akshay17 at olemiss.edu
<http://www.gromacs.org/mailman/listinfo/gmx-users>
Tel: 662-915-1286 (office); Web: www.olemiss.edu

|*-----Original Message-----*|*From: David van der Spoel [mailto:spoel
at xray.bmc.uu.se
<http://www.gromacs.org/mailman/listinfo/gmx-users>]*|*Sent: Tuesday,
April 18, 2006 12:22 AM*|*To: akshay17 at olemiss.edu
<http://www.gromacs.org/mailman/listinfo/gmx-users>; Discussion list
for GROMACS users*|*Subject: Re: [gmx-users] GROMACS 3.3.1
installation on SGI (Irix): 2*|**|*Akshay Patny wrote:*|>* Hi*|>* Hi
ALl*|>**|>* I read through some of the e-mails of B. Nataraj and Erik
Lindahl for*|>* similar problem on compiling of GROMACS 3.3.1 on SGI
IRIX.*|>**|>* As my error also pointed to a problem in
"gmx_fft_fftw3.c", I replaced*|*the*|>* 'void' with 'char' in the line
150 of the file, as suggested.*|>**|>* I got the errors exactly the
same as B. Nataraj got after doing this*|>* modification, which is
listed at*|>* http://www.gromacs.org/pipermail/gmx-users/2006-April/020969.html*|>**|>*
The same error is given below. I could not understand how to fix
this*|*error*|>* and run GROMACS successfully.*|>**|>* Dr. Erik
Lindahl wrote that: "As far as I can see that file is perfectly*|>*
valid ANSI C - there is no executable statement in the
declaration*|*section."*|>**|>* However, I still do not know how to
fix this?*|>**|**|*there is a double semicolon on one of the lines
before it. please remove*|*it and retry.*|**|>* Please help.*|>**|>*
Regards*|>* Akshay*|>**|>* Error is given
below:*|>**|*___________________________________________________________________________*|*_*|>**|>*
cc-1241 cc: ERROR File = gmx_chi.c, Line = 1031*|>*   A declaration
cannot appear after an executable statement in a block.*|>**|>*
static real core_frac=0.5 ;*|>*     ^*|>**|>* cc-1241 cc: ERROR File =
gmx_chi.c, Line = 1032*|>*   A declaration cannot appear after an
executable statement in a block.*|>**|>*     t_pargs pa[] = {*|>*
^*|>**|>* cc-1241 cc: ERROR File = gmx_chi.c, Line = 1073*|>*   A
declaration cannot appear after an executable statement in a
block.*|>**|>*     FILE       *log;*|>*     ^*|>**|>* cc-1241 cc:
ERROR File = gmx_chi.c, Line = 1074*|>*   A declaration cannot appear
after an executable statement in a block.*|>**|>*     int
natoms,nlist,naa,idum,nbin;*|>*     ^*|>**|>* cc-1241 cc: ERROR File =
gmx_chi.c, Line = 1075*|>*   A declaration cannot appear after an
executable statement in a block.*|>**|>*     t_atoms    atoms;*|>*
^*|>**|>* cc-1241 cc: ERROR File = gmx_chi.c, Line = 1076*|>*   A
declaration cannot appear after an executable statement in a
block.*|>**|>*     rvec       *x;*|>*     ^*|>**|>* cc-1241 cc: ERROR
File = gmx_chi.c, Line = 1077*|>*   A declaration cannot appear after
an executable statement in a block.*|>**|>*     matrix     box;*|>*
 ^*|>**|>* cc-1241 cc: ERROR File = gmx_chi.c, Line = 1078*|>*   A
declaration cannot appear after an executable statement in a
block.*|>**|>*     char       title[256],grpname[256];*|>*
^*|>**|>* cc-1241 cc: ERROR File = gmx_chi.c, Line = 1079*|>*   A
declaration cannot appear after an executable statement in a
block.*|>**|>*     t_dlist    *dlist;*|>*     ^*|>**|>* cc-1241 cc:
ERROR File = gmx_chi.c, Line = 1080*|>*   A declaration cannot appear
after an executable statement in a block.*|>**|>*     char
**aa;*|>*     ^*|>**|>* cc-1241 cc: ERROR File = gmx_chi.c, Line =
1081*|>*   A declaration cannot appear after an executable statement
in a block.*|>**|>*     bool       bChi,bCorr,bSSHisto;*|>*
^*|>**|>* cc-1241 cc: ERROR File = gmx_chi.c, Line = 1082*|>*   A
declaration cannot appear after an executable statement in a
block.*|>**|>*     bool       bDo_rt, bDo_oh, bDo_ot, bDo_jc ;*|>*
^*|>**|>* cc-1241 cc: ERROR File = gmx_chi.c, Line = 1083*|>*   A
declaration cannot appear after an executable statement in a
block.*|>**|>*     real       dt=0, traj_t_ns;*|>*     ^*|>**|>*
cc-1241 cc: ERROR File = gmx_chi.c, Line = 1085*|>*   A declaration
cannot appear after an executable statement in a block.*|>**|>*
atom_id    isize,*index;*|>*     ^*|>**|>* cc-1241 cc: ERROR File =
gmx_chi.c, Line = 1086*|>*   A declaration cannot appear after an
executable statement in a block.*|>**|>*     int
ndih,nactdih,nf;*|>*     ^*|>**|>* cc-1241 cc: ERROR File = gmx_chi.c,
Line = 1087*|>*   A declaration cannot appear after an executable
statement in a block.*|>**|>*     real
**dih,*trans_frac,*aver_angle,*time;*|>*     ^*|>**|>* cc-1241 cc:
ERROR File = gmx_chi.c, Line = 1088*|>*   A declaration cannot appear
after an executable statement in a block.*|>**|>*     int
i,j,**chi_lookup,*xity;*|>*     ^*|>**|>* cc-1241 cc: ERROR File =
gmx_chi.c, Line = 1090*|>*   A declaration cannot appear after an
executable statement in a block.*|>**|>*     t_filenm  fnm[] = {*|>*
  ^*|>**|>* cc-1241 cc: ERROR File = gmx_chi.c, Line = 1106*|>*   A
declaration cannot appear after an executable statement in a
block.*|>**|>*     int     npargs;*|>*     ^*|>**|>* cc-1241 cc: ERROR
File = gmx_chi.c, Line = 1107*|>*   A declaration cannot appear after
an executable statement in a block.*|>**|>*     t_pargs *ppa;*|>*
^*|>**|>* 20 errors detected in the compilation of "gmx_chi.c".*|>*
*** Error code 1 (bu21)*|>* *** Error code 1 (bu21)*|>* *** Error code
1*|>**|*(bu21)_____________________________________________________________________*|*_*|>*
______*|>**|>**|>* Akshay Patny*|>**|>* Graduate Research
Assistant*|>* Faser Hall 417, Department of Medicinal Chemistry*|>*
Research Institute of Pharmaceutical Sciences*|>* University of
Mississippi*|>* University, MS 38677*|>* E-mail: akshay17 at
olemiss.edu <http://www.gromacs.org/mailman/listinfo/gmx-users>*|>*
Tel: 662-915-1286 (office); Web: www.olemiss.edu*|>**|>**|>*
_______________________________________________*|>* gmx-users mailing
list    gmx-users at gromacs.org
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Read http://www.gromacs.org/mailing_lists/users.php*|**|**|*--*|*David.*|*________________________________________________________________________*|*David
van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,*|*Dept.
of Cell and Molecular Biology, Uppsala University.*|*Husargatan 3, Box
596,  	75124 Uppsala, Sweden*|*phone:	46 18 471 4205		fax: 46 18 511
755*|*spoel at xray.bmc.uu.se
<http://www.gromacs.org/mailman/listinfo/gmx-users>	spoel at
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-- 
James
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