Discussion:
SGI installation problem
(too old to reply)
Siavoush Dastmalchi
2008-03-15 14:14:04 UTC
Permalink
Hi there,

This is a bit funny that I am posting this problem again, but I am hopping that I may find a solution. I recently down loaded gromacs-3.3.3 and was trying to install it on my sgi computer. I get error massage (as shown below). It seems that many others also had such a problem, so wondering if some one can help me out with this.

Cheers, Siavoush

source='nsc.c' object='nsc.lo' libtool=yes \
DEPDIR=.deps depmode=sgi /bin/sh ../../config/depcomp \
/bin/sh ../../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I../../src -I../../include -DGMXLIBDIR=\"/usr/local/gromacs/share/top\" -I/usr/local/include -r12000 -mips4 -O3 -OPT:IEEE_arithmetic=3 -OPT:rsqrt=ON -SWP:loop_overhead -INLINE:=ON -LNO:opt=1 -LNO:ou_further=3 -OPT:Olimit=0:roundoff=3:alias=typed -woff 1174 -D__INLINE_INTRINSICS -c -o nsc.lo nsc.c
cc -DHAVE_CONFIG_H -I. -I../../src -I../../include "-DGMXLIBDIR=\"/usr/local/gromacs/share/top\"" -I/usr/local/include -r12000 -mips4 -O3 -OPT:IEEE_arithmetic=3 -OPT:rsqrt=ON -SWP:loop_overhead -INLINE:=ON -LNO:opt=1 -LNO:ou_further=3 -OPT:Olimit=0:roundoff=3:alias=typed -woff 1174 -D__INLINE_INTRINSICS -c nsc.c -Wp,-MDupdate,.deps/nsc.TPlo -o nsc.o
cc-1028 cc: ERROR File = nsc.c, Line = 729
The expression used must have a constant value.
rvec xxi = { xi, yi, zi };
^
cc-1028 cc: ERROR File = nsc.c, Line = 729
The expression used must have a constant value.
rvec xxi = { xi, yi, zi };
^
cc-1028 cc: ERROR File = nsc.c, Line = 729
The expression used must have a constant value.
rvec xxi = { xi, yi, zi };
^
3 errors detected in the compilation of "nsc.c".
*** Error code 1 (bu21)
*** Error code 1 (bu21)
*** Error code 1 (bu21)
*** Error code 1 (bu21)
David van der Spoel
2008-03-15 16:45:46 UTC
Permalink
Post by Siavoush Dastmalchi
Hi there,
This is a bit funny that I am posting this problem again, but I am hopping that I may find a solution. I recently down loaded gromacs-3.3.3 and was trying to install it on my sgi computer. I get error massage (as shown below). It seems that many others also had such a problem, so wondering if some one can help me out with this.
Cheers, Siavoush
source='nsc.c' object='nsc.lo' libtool=yes \
DEPDIR=.deps depmode=sgi /bin/sh ../../config/depcomp \
/bin/sh ../../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I../../src -I../../include -DGMXLIBDIR=\"/usr/local/gromacs/share/top\" -I/usr/local/include -r12000 -mips4 -O3 -OPT:IEEE_arithmetic=3 -OPT:rsqrt=ON -SWP:loop_overhead -INLINE:=ON -LNO:opt=1 -LNO:ou_further=3 -OPT:Olimit=0:roundoff=3:alias=typed -woff 1174 -D__INLINE_INTRINSICS -c -o nsc.lo nsc.c
cc -DHAVE_CONFIG_H -I. -I../../src -I../../include "-DGMXLIBDIR=\"/usr/local/gromacs/share/top\"" -I/usr/local/include -r12000 -mips4 -O3 -OPT:IEEE_arithmetic=3 -OPT:rsqrt=ON -SWP:loop_overhead -INLINE:=ON -LNO:opt=1 -LNO:ou_further=3 -OPT:Olimit=0:roundoff=3:alias=typed -woff 1174 -D__INLINE_INTRINSICS -c nsc.c -Wp,-MDupdate,.deps/nsc.TPlo -o nsc.o
cc-1028 cc: ERROR File = nsc.c, Line = 729
The expression used must have a constant value.
rvec xxi = { xi, yi, zi };
^
cc-1028 cc: ERROR File = nsc.c, Line = 729
The expression used must have a constant value.
rvec xxi = { xi, yi, zi };
^
cc-1028 cc: ERROR File = nsc.c, Line = 729
The expression used must have a constant value.
rvec xxi = { xi, yi, zi };
replace the code at line 729 by

rvec xxi;
xxi[XX] = xi;
xxi[YY] = yi;
xxi[ZZ] = zi;
Post by Siavoush Dastmalchi
^
3 errors detected in the compilation of "nsc.c".
*** Error code 1 (bu21)
*** Error code 1 (bu21)
*** Error code 1 (bu21)
*** Error code 1 (bu21)
_______________________________________________
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Please search the archive at http://www.gromacs.org/search before posting!
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--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
Siavoush Dastmalchi
2008-03-16 05:03:16 UTC
Permalink
Hi,

Thanks to David for his suggestion. Now I have the following error. It is a bit of shame that I am hassling you, but I want GMX to work on my sgi.



Cheers, Siavoush



Here is the error message:

gmx_spatial.c -Wp,-MDupdate,.deps/gmx_spatial.TPlo -o gmx_spatial.o
cc-1028 cc: ERROR File = gmx_spatial.c, Line = 110
The expression used must have a constant value.
{ "-pbc", bPBC, etBOOL, {&bPBC},
^
cc-1028 cc: ERROR File = gmx_spatial.c, Line = 112
The expression used must have a constant value.
{ "-div", bCALCDIV, etBOOL, {&bCALCDIV},
^
cc-1028 cc: ERROR File = gmx_spatial.c, Line = 114
The expression used must have a constant value.
{ "-ign", iIGNOREOUTER, etINT, {&iIGNOREOUTER},
^
cc-1028 cc: ERROR File = gmx_spatial.c, Line = 118
The expression used must have a constant value.
{ "-bin", rBINWIDTH, etREAL, {&rBINWIDTH},
^
cc-1028 cc: ERROR File = gmx_spatial.c, Line = 120
The expression used must have a constant value.
{ "-nab", iNAB, etINT, {&iNAB},
^
5 errors detected in the compilation of "gmx_spatial.c".


________________________________

From: gmx-users-bounces at gromacs.org on behalf of David van der Spoel
Sent: Sat 2008/03/15 08:15 ?.?
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] SGI installation problem
Post by Siavoush Dastmalchi
Hi there,
This is a bit funny that I am posting this problem again, but I am hopping that I may find a solution. I recently down loaded gromacs-3.3.3 and was trying to install it on my sgi computer. I get error massage (as shown below). It seems that many others also had such a problem, so wondering if some one can help me out with this.
Cheers, Siavoush
source='nsc.c' object='nsc.lo' libtool=yes \
DEPDIR=.deps depmode=sgi /bin/sh ../../config/depcomp \
/bin/sh ../../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I../../src -I../../include -DGMXLIBDIR=\"/usr/local/gromacs/share/top\" -I/usr/local/include -r12000 -mips4 -O3 -OPT:IEEE_arithmetic=3 -OPT:rsqrt=ON -SWP:loop_overhead -INLINE:=ON -LNO:opt=1 -LNO:ou_further=3 -OPT:Olimit=0:roundoff=3:alias=typed -woff 1174 -D__INLINE_INTRINSICS -c -o nsc.lo nsc.c
cc -DHAVE_CONFIG_H -I. -I../../src -I../../include "-DGMXLIBDIR=\"/usr/local/gromacs/share/top\"" -I/usr/local/include -r12000 -mips4 -O3 -OPT:IEEE_arithmetic=3 -OPT:rsqrt=ON -SWP:loop_overhead -INLINE:=ON -LNO:opt=1 -LNO:ou_further=3 -OPT:Olimit=0:roundoff=3:alias=typed -woff 1174 -D__INLINE_INTRINSICS -c nsc.c -Wp,-MDupdate,.deps/nsc.TPlo -o nsc.o
cc-1028 cc: ERROR File = nsc.c, Line = 729
The expression used must have a constant value.
rvec xxi = { xi, yi, zi };
^
cc-1028 cc: ERROR File = nsc.c, Line = 729
The expression used must have a constant value.
rvec xxi = { xi, yi, zi };
^
cc-1028 cc: ERROR File = nsc.c, Line = 729
The expression used must have a constant value.
rvec xxi = { xi, yi, zi };
replace the code at line 729 by

rvec xxi;
xxi[XX] = xi;
xxi[YY] = yi;
xxi[ZZ] = zi;
Post by Siavoush Dastmalchi
^
3 errors detected in the compilation of "nsc.c".
*** Error code 1 (bu21)
*** Error code 1 (bu21)
*** Error code 1 (bu21)
*** Error code 1 (bu21)
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se <http://folding.bmc.uu.se/>
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
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Can't post? Read http://www.gromacs.org/mailing_lists/users.php
David van der Spoel
2008-03-16 08:00:26 UTC
Permalink
Post by Siavoush Dastmalchi
Hi,
Thanks to David for his suggestion. Now I have the following error. It is a bit of shame that I am hassling you, but I want GMX to work on my sgi.
Cheers, Siavoush
gmx_spatial.c -Wp,-MDupdate,.deps/gmx_spatial.TPlo -o gmx_spatial.o
cc-1028 cc: ERROR File = gmx_spatial.c, Line = 110
The expression used must have a constant value.
{ "-pbc", bPBC, etBOOL, {&bPBC},
^
cc-1028 cc: ERROR File = gmx_spatial.c, Line = 112
The expression used must have a constant value.
{ "-div", bCALCDIV, etBOOL, {&bCALCDIV},
^
cc-1028 cc: ERROR File = gmx_spatial.c, Line = 114
The expression used must have a constant value.
{ "-ign", iIGNOREOUTER, etINT, {&iIGNOREOUTER},
^
cc-1028 cc: ERROR File = gmx_spatial.c, Line = 118
The expression used must have a constant value.
{ "-bin", rBINWIDTH, etREAL, {&rBINWIDTH},
^
cc-1028 cc: ERROR File = gmx_spatial.c, Line = 120
The expression used must have a constant value.
{ "-nab", iNAB, etINT, {&iNAB},
^
5 errors detected in the compilation of "gmx_spatial.c".
Please replace all of these by FALSE (in capital).
--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
Siavoush Dastmalchi
2008-03-16 10:42:39 UTC
Permalink
Hi there,
Now I am getting the following error. I can see that others had this problem before and there are couple of solutions in the archive suggested by the list. I was wondering which one should I consider. Some suggestions apparently didn't work, but others , I am not sure.
Many thanks,
Siavoush

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)


________________________________

From: gmx-users-bounces at gromacs.org on behalf of David van der Spoel
Sent: Sun 2008/03/16 11:30 ?.?
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] SGI installation problem
Post by Siavoush Dastmalchi
Hi,
Thanks to David for his suggestion. Now I have the following error. It is a bit of shame that I am hassling you, but I want GMX to work on my sgi.
Cheers, Siavoush
gmx_spatial.c -Wp,-MDupdate,.deps/gmx_spatial.TPlo -o gmx_spatial.o
cc-1028 cc: ERROR File = gmx_spatial.c, Line = 110
The expression used must have a constant value.
{ "-pbc", bPBC, etBOOL, {&bPBC},
^
cc-1028 cc: ERROR File = gmx_spatial.c, Line = 112
The expression used must have a constant value.
{ "-div", bCALCDIV, etBOOL, {&bCALCDIV},
^
cc-1028 cc: ERROR File = gmx_spatial.c, Line = 114
The expression used must have a constant value.
{ "-ign", iIGNOREOUTER, etINT, {&iIGNOREOUTER},
^
cc-1028 cc: ERROR File = gmx_spatial.c, Line = 118
The expression used must have a constant value.
{ "-bin", rBINWIDTH, etREAL, {&rBINWIDTH},
^
cc-1028 cc: ERROR File = gmx_spatial.c, Line = 120
The expression used must have a constant value.
{ "-nab", iNAB, etINT, {&iNAB},
^
5 errors detected in the compilation of "gmx_spatial.c".
Please replace all of these by FALSE (in capital).

--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se <http://folding.bmc.uu.se/>
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Erik Lindahl
2008-03-16 11:56:02 UTC
Permalink
Hi,

One option would simply be to remove make_edi from Makefile.am.
Unfortunately this tool has proven to be a bit buggy in the compile
stage, and you won't need it for any normal simulations.

The other fix would be to create separate static variables to use in
the list for reading options, and assembling then into evStepOptions[]
after the fact.

Cheers,

Erik
Post by Siavoush Dastmalchi
Hi there,
Now I am getting the following error. I can see that others had this
problem before and there are couple of solutions in the archive
suggested by the list. I was wondering which one should I consider.
Some suggestions apparently didn't work, but others , I am not sure.
Many thanks,
Siavoush
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)
________________________________
From: gmx-users-bounces at gromacs.org on behalf of David van der Spoel
Sent: Sun 2008/03/16 11:30 ?.?
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] SGI installation problem
Post by Siavoush Dastmalchi
Hi,
Thanks to David for his suggestion. Now I have the following error.
It is a bit of shame that I am hassling you, but I want GMX to work
on my sgi.
Cheers, Siavoush
gmx_spatial.c -Wp,-MDupdate,.deps/gmx_spatial.TPlo -o gmx_spatial.o
cc-1028 cc: ERROR File = gmx_spatial.c, Line = 110
The expression used must have a constant value.
{ "-pbc", bPBC, etBOOL, {&bPBC},
^
cc-1028 cc: ERROR File = gmx_spatial.c, Line = 112
The expression used must have a constant value.
{ "-div", bCALCDIV, etBOOL, {&bCALCDIV},
^
cc-1028 cc: ERROR File = gmx_spatial.c, Line = 114
The expression used must have a constant value.
{ "-ign", iIGNOREOUTER, etINT, {&iIGNOREOUTER},
^
cc-1028 cc: ERROR File = gmx_spatial.c, Line = 118
The expression used must have a constant value.
{ "-bin", rBINWIDTH, etREAL, {&rBINWIDTH},
^
cc-1028 cc: ERROR File = gmx_spatial.c, Line = 120
The expression used must have a constant value.
{ "-nab", iNAB, etINT, {&iNAB},
^
5 errors detected in the compilation of "gmx_spatial.c".
Please replace all of these by FALSE (in capital).
--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala
University.
+4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
<http://folding.bmc.uu.se/>
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Siavoush Dastmalchi
2008-03-16 12:14:24 UTC
Permalink
Hi,
I did the following changes and it seems that problem has been fixed. But, then again I got the error saying that:
syntax error in makefile line xxx ( I can't remember the exact error message now).
Here is the changes on the make_edi file:

{ evStepOptions[evLINFIX], FALSE, etSTR, {&evParams[evLINFIX]}, was changed to:
{"-linfix", FALSE, etSTR, {&evSelections[evLINFIX]},

I am starting over again from configuration step and will let you know the result.
By the way, I got the syntax error for makefile at the same line when I was doing distclean.

Cheers, Siavoush

________________________________

From: gmx-users-bounces at gromacs.org on behalf of Erik Lindahl
Sent: Sun 2008/03/16 03:26 ?.?
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] SGI installation problem



Hi,

One option would simply be to remove make_edi from Makefile.am.
Unfortunately this tool has proven to be a bit buggy in the compile
stage, and you won't need it for any normal simulations.

The other fix would be to create separate static variables to use in
the list for reading options, and assembling then into evStepOptions[]
after the fact.

Cheers,

Erik
Post by Siavoush Dastmalchi
Hi there,
Now I am getting the following error. I can see that others had this
problem before and there are couple of solutions in the archive
suggested by the list. I was wondering which one should I consider.
Some suggestions apparently didn't work, but others , I am not sure.
Many thanks,
Siavoush
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)
________________________________
From: gmx-users-bounces at gromacs.org on behalf of David van der Spoel
Sent: Sun 2008/03/16 11:30 ?.?
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] SGI installation problem
Post by Siavoush Dastmalchi
Hi,
Thanks to David for his suggestion. Now I have the following error.
It is a bit of shame that I am hassling you, but I want GMX to work
on my sgi.
Cheers, Siavoush
gmx_spatial.c -Wp,-MDupdate,.deps/gmx_spatial.TPlo -o gmx_spatial.o
cc-1028 cc: ERROR File = gmx_spatial.c, Line = 110
The expression used must have a constant value.
{ "-pbc", bPBC, etBOOL, {&bPBC},
^
cc-1028 cc: ERROR File = gmx_spatial.c, Line = 112
The expression used must have a constant value.
{ "-div", bCALCDIV, etBOOL, {&bCALCDIV},
^
cc-1028 cc: ERROR File = gmx_spatial.c, Line = 114
The expression used must have a constant value.
{ "-ign", iIGNOREOUTER, etINT, {&iIGNOREOUTER},
^
cc-1028 cc: ERROR File = gmx_spatial.c, Line = 118
The expression used must have a constant value.
{ "-bin", rBINWIDTH, etREAL, {&rBINWIDTH},
^
cc-1028 cc: ERROR File = gmx_spatial.c, Line = 120
The expression used must have a constant value.
{ "-nab", iNAB, etINT, {&iNAB},
^
5 errors detected in the compilation of "gmx_spatial.c".
Please replace all of these by FALSE (in capital).
--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala
University.
+4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se <http://folding.bmc.uu.se/>
<http://folding.bmc.uu.se/>
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Siavoush Dastmalchi
2008-03-16 13:30:57 UTC
Permalink
Hi,
As I mentioned before, the installation stopped with the error shown below.
Looking for your kind attentions.
Cheers, Siavoush

Making all in contrib
Making all in admin
Making all in scripts
make: file 'Makefile' line 417: syntax error
*** Error code 1 (bu21)


________________________________

From: gmx-users-bounces at gromacs.org on behalf of Siavoush Dastmalchi
Sent: Sun 2008/03/16 03:44 ?.?
To: gmx-users at gromacs.org
Subject: RE: [gmx-users] SGI installation problem



Hi,
I did the following changes and it seems that problem has been fixed. But, then again I got the error saying that:
syntax error in makefile line xxx ( I can't remember the exact error message now).
Here is the changes on the make_edi file:

{ evStepOptions[evLINFIX], FALSE, etSTR, {&evParams[evLINFIX]}, was changed to:
{"-linfix", FALSE, etSTR, {&evSelections[evLINFIX]},

I am starting over again from configuration step and will let you know the result.
By the way, I got the syntax error for makefile at the same line when I was doing distclean.

Cheers, Siavoush

________________________________

From: gmx-users-bounces at gromacs.org on behalf of Erik Lindahl
Sent: Sun 2008/03/16 03:26 ?.?
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] SGI installation problem



Hi,

One option would simply be to remove make_edi from Makefile.am.
Unfortunately this tool has proven to be a bit buggy in the compile
stage, and you won't need it for any normal simulations.

The other fix would be to create separate static variables to use in
the list for reading options, and assembling then into evStepOptions[]
after the fact.

Cheers,

Erik
Post by Siavoush Dastmalchi
Hi there,
Now I am getting the following error. I can see that others had this
problem before and there are couple of solutions in the archive
suggested by the list. I was wondering which one should I consider.
Some suggestions apparently didn't work, but others , I am not sure.
Many thanks,
Siavoush
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)
________________________________
From: gmx-users-bounces at gromacs.org on behalf of David van der Spoel
Sent: Sun 2008/03/16 11:30 ?.?
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] SGI installation problem
Post by Siavoush Dastmalchi
Hi,
Thanks to David for his suggestion. Now I have the following error.
It is a bit of shame that I am hassling you, but I want GMX to work
on my sgi.
Cheers, Siavoush
gmx_spatial.c -Wp,-MDupdate,.deps/gmx_spatial.TPlo -o gmx_spatial.o
cc-1028 cc: ERROR File = gmx_spatial.c, Line = 110
The expression used must have a constant value.
{ "-pbc", bPBC, etBOOL, {&bPBC},
^
cc-1028 cc: ERROR File = gmx_spatial.c, Line = 112
The expression used must have a constant value.
{ "-div", bCALCDIV, etBOOL, {&bCALCDIV},
^
cc-1028 cc: ERROR File = gmx_spatial.c, Line = 114
The expression used must have a constant value.
{ "-ign", iIGNOREOUTER, etINT, {&iIGNOREOUTER},
^
cc-1028 cc: ERROR File = gmx_spatial.c, Line = 118
The expression used must have a constant value.
{ "-bin", rBINWIDTH, etREAL, {&rBINWIDTH},
^
cc-1028 cc: ERROR File = gmx_spatial.c, Line = 120
The expression used must have a constant value.
{ "-nab", iNAB, etINT, {&iNAB},
^
5 errors detected in the compilation of "gmx_spatial.c".
Please replace all of these by FALSE (in capital).
--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala
University.
+4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se <http://folding.bmc.uu.se/> <http://folding.bmc.uu.se/>
<http://folding.bmc.uu.se/>
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
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http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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_______________________________________________
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http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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Can't post? Read http://www.gromacs.org/mailing_lists/users.php


_______________________________________________
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http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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David van der Spoel
2008-03-16 13:37:01 UTC
Permalink
Post by Siavoush Dastmalchi
Hi,
As I mentioned before, the installation stopped with the error shown below.
Looking for your kind attentions.
Cheers, Siavoush
Making all in contrib
Making all in admin
Making all in scripts
make: file 'Makefile' line 417: syntax error
*** Error code 1 (bu21)
Try this Makefile in the scripts directory.
--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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Siavoush Dastmalchi
2008-03-16 14:16:54 UTC
Permalink
Hi David,

I did as following and still getting the same error:

% make -f scripts/Makefile

There are some minor differences (apart from those related to the specifications and paths in my system) between the file that you sent me and the one in the script directory. May be the way that I trying to use the Makefile in the script directory is not OK. Do I need to do configuration step again and then use the scripts/Makefile?
I have attached the Makefile in the script directory just in case.

Regards, Siavoush


________________________________

From: gmx-users-bounces at gromacs.org on behalf of David van der Spoel
Sent: Sun 2008/03/16 05:07 ?.?
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] SGI installation problem
Post by Siavoush Dastmalchi
Hi,
As I mentioned before, the installation stopped with the error shown below.
Looking for your kind attentions.
Cheers, Siavoush
Making all in contrib
Making all in admin
Making all in scripts
make: file 'Makefile' line 417: syntax error
*** Error code 1 (bu21)
Try this Makefile in the scripts directory.

--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se <http://folding.bmc.uu.se/>


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Erik Lindahl
2008-03-19 09:09:51 UTC
Permalink
Hi,

I'm not quite sure what David was thinking, but Makefiles are created
on-the-fly with automake/autoconf and tailored to the commands on your
system, so there is absolutely no way a Mac makefile will work on an
SGI :-)

An error like

make: file 'Makefile' line 417: syntax error
*** Error code 1 (bu21)

typically means you've edited the makefile manually, or moved the
source. Try a "make distclean" and start over from scratch with ./
configure!

Cheers,

Erik
Post by Siavoush Dastmalchi
Hi David,
% make -f scripts/Makefile
There are some minor differences (apart from those related to the
specifications and paths in my system) between the file that you
sent me and the one in the script directory. May be the way that I
trying to use the Makefile in the script directory is not OK. Do I
need to do configuration step again and then use the scripts/Makefile?
I have attached the Makefile in the script directory just in case.
Regards, Siavoush
________________________________
From: gmx-users-bounces at gromacs.org on behalf of David van der Spoel
Sent: Sun 2008/03/16 05:07 ?.?
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] SGI installation problem
Post by Siavoush Dastmalchi
Hi,
As I mentioned before, the installation stopped with the error shown below.
Looking for your kind attentions.
Cheers, Siavoush
Making all in contrib
Making all in admin
Making all in scripts
make: file 'Makefile' line 417: syntax error
*** Error code 1 (bu21)
Try this Makefile in the scripts directory.
--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala
University.
+4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
<http://folding.bmc.uu.se/>
<winmail.dat>_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
------------
Erik Lindahl <lindahl at cbr.su.se> Backup: <erik.lindahl at gmail.com>
Assistant Professor, Computational Structural Biology
Center for Biomembrane Research, Dept. Biochemistry & Biophysics
Stockholm University, SE-106 91 Stockholm, Sweden
Tel: +46(0)8164675 Mobile: +46(0)704218767 Fax: mail a PDF instead
Siavoush Dastmalchi
2008-03-19 13:25:21 UTC
Permalink
Hi,

Thanks for the suggestion and I am sorry that didn't let the list know that the problem had been fixed. (I haven't used the mdrun yet, but the other stuff seems working) Thanks to the Makefile that I have received from David. I compared that file with the one created in the script directory and then did some changes to it, and it worked for me. I need to add that I tried couple of times starting from ./configuration step. I was also getting the same error while trying the "make distclean". It is funny, but true though that the Makefile that I used finally in the script directory is a hybrid created under Sgi and Mac, but did work.

Once again thanks for your concerns.

Cheers, Siavoush

________________________________

From: gmx-users-bounces at gromacs.org on behalf of Erik Lindahl
Sent: Wed 2008/03/19 12:39 ?.?
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] SGI installation problem



Hi,

I'm not quite sure what David was thinking, but Makefiles are created
on-the-fly with automake/autoconf and tailored to the commands on your
system, so there is absolutely no way a Mac makefile will work on an
SGI :-)

An error like

make: file 'Makefile' line 417: syntax error
*** Error code 1 (bu21)

typically means you've edited the makefile manually, or moved the
source. Try a "make distclean" and start over from scratch with ./
configure!

Cheers,

Erik
Post by Siavoush Dastmalchi
Hi David,
% make -f scripts/Makefile
There are some minor differences (apart from those related to the
specifications and paths in my system) between the file that you
sent me and the one in the script directory. May be the way that I
trying to use the Makefile in the script directory is not OK. Do I
need to do configuration step again and then use the scripts/Makefile?
I have attached the Makefile in the script directory just in case.
Regards, Siavoush
________________________________
From: gmx-users-bounces at gromacs.org on behalf of David van der Spoel
Sent: Sun 2008/03/16 05:07 ?.?
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] SGI installation problem
Post by Siavoush Dastmalchi
Hi,
As I mentioned before, the installation stopped with the error shown below.
Looking for your kind attentions.
Cheers, Siavoush
Making all in contrib
Making all in admin
Making all in scripts
make: file 'Makefile' line 417: syntax error
*** Error code 1 (bu21)
Try this Makefile in the scripts directory.
--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala
University.
+4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se <http://folding.bmc.uu.se/>
<http://folding.bmc.uu.se/>
<winmail.dat>_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
------------
Erik Lindahl <lindahl at cbr.su.se> Backup: <erik.lindahl at gmail.com>
Assistant Professor, Computational Structural Biology
Center for Biomembrane Research, Dept. Biochemistry & Biophysics
Stockholm University, SE-106 91 Stockholm, Sweden
Tel: +46(0)8164675 Mobile: +46(0)704218767 Fax: mail a PDF instead




_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

David van der Spoel
2008-03-16 12:27:43 UTC
Permalink
Post by Erik Lindahl
Hi,
One option would simply be to remove make_edi from Makefile.am.
Unfortunately this tool has proven to be a bit buggy in the compile
stage, and you won't need it for any normal simulations.
The other fix would be to create separate static variables to use in the
list for reading options, and assembling then into evStepOptions[] after
the fact.
I've replaced the arrays by static strings and committed to CVS (3.3 and
head branches). If one to the make_edi developers volunteers to clean it
up, you're welcome.
Post by Erik Lindahl
Cheers,
Erik
Post by Siavoush Dastmalchi
Hi there,
Now I am getting the following error. I can see that others had this
problem before and there are couple of solutions in the archive
suggested by the list. I was wondering which one should I consider.
Some suggestions apparently didn't work, but others , I am not sure.
Many thanks,
Siavoush
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)
________________________________
From: gmx-users-bounces at gromacs.org on behalf of David van der Spoel
Sent: Sun 2008/03/16 11:30 ?.?
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] SGI installation problem
Post by Siavoush Dastmalchi
Hi,
Thanks to David for his suggestion. Now I have the following error.
It is a bit of shame that I am hassling you, but I want GMX to work
on my sgi.
Cheers, Siavoush
gmx_spatial.c -Wp,-MDupdate,.deps/gmx_spatial.TPlo -o gmx_spatial.o
cc-1028 cc: ERROR File = gmx_spatial.c, Line = 110
The expression used must have a constant value.
{ "-pbc", bPBC, etBOOL, {&bPBC},
^
cc-1028 cc: ERROR File = gmx_spatial.c, Line = 112
The expression used must have a constant value.
{ "-div", bCALCDIV, etBOOL, {&bCALCDIV},
^
cc-1028 cc: ERROR File = gmx_spatial.c, Line = 114
The expression used must have a constant value.
{ "-ign", iIGNOREOUTER, etINT, {&iIGNOREOUTER},
^
cc-1028 cc: ERROR File = gmx_spatial.c, Line = 118
The expression used must have a constant value.
{ "-bin", rBINWIDTH, etREAL, {&rBINWIDTH},
^
cc-1028 cc: ERROR File = gmx_spatial.c, Line = 120
The expression used must have a constant value.
{ "-nab", iNAB, etINT, {&iNAB},
^
5 errors detected in the compilation of "gmx_spatial.c".
Please replace all of these by FALSE (in capital).
--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
<http://folding.bmc.uu.se/>
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use thewww
interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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