AMBER Archive (2006)

Subject: RE: AMBER: Error in sysdepend.c?

From: Shin, John Y CONTRACTOR WRAIR-Wash DC (John.Shin_at_AMEDD.ARMY.MIL)
Date: Mon Dec 18 2006 - 14:27:24 CST

Thanks for the response Dave.

I added "-DSYSV" to the CFLAGS variable in config.h, and that allowed
compilation to continue quite a bit further until the following error
was encountered while compiling leap:

-----------------------------------
gcc -o xaLeap basics.o sysdepend.o stringExtra.o varArray.o getline.o
avl.o pdb_format.o pdb_read.o pdb_sprntf.o pdb_sscanf.o pdb_write.o
vector.o zMatrix.o sort.o bag.o hash.o dictionary.o database.o nVector.o
ring.o matrix.o fortran.o displayer.o assoc.o atom.o byteArray.o
collection.o container.o internal.o list.o loop.o molecule.o oDouble.o
oInteger.o oString.o objekt.o parmSet.o residue.o unit.o unitio.o
tripos.o graphUtil.o select.o amber.o build.o elements.o library.o
chirality.o minimizer.o model.o parmLib.o pdbFile.o tools.o variables.o
parser.o help.o helptext.o octree.o commands.o mathop.o block.o
restraint.o hybrid.o xTank.o xAction.o x3d.o xBasics.o xaLeapc.o
xaUnitEditor.o xaTable.o xaAtomTable.o XrawRegister.o xaCommand.o
xaTools.o xaAtomParmTable.o xaBondParmTable.o xaAngleParmTable.o
xaParmEditor.o xaTorsionParmTable.o xaImproperParmTable.o
xaHBondParmTable.o ../Xraw/libXaw.a ../Wc/libWcLeap.a ../Xpm/libXpm.a
../Xmu/libXmu.a -L /usr/X11R6/lib -lXt -lXext -lSM -lICE -lx11 -lm
-lpthread m4 xaLeap.rm4 > XaLeap_wcl

m4:xaLeap.rm4:993 pushed back more than 4096 chars
define(TABLE_SHELL,XaLeap*$1TableShell.wcClassName: TopLevelShell
XaLeap*$1TableShell.wcChildren: $1TablePanel
XaLeap*$1TableShell.wcCallback: XATRegisterShell()
XaLeap*$1TableShell.wcPopups: findDialog
XaLeap*$1TableShell.title: XLEaP: $2
XaLeap*$1TableShell.iconName $2
XaLeap*$1TableShell.iconPixmap: table1
XaLeap*$1TableShell.destroyCallback: $3 WcDestroyCB( .*findDialog )

XaLeap*$1TableShell.wcAfterChildren: \
        XASetPopdown( .*findDialog .*$1Find .*findDialog*cancel)

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!! The name of this widget is using in file xaTable.c (XATSaveTable)
!!
DIALOG_QUEST_OK_CANCEL(verify_save_none_corect_table,\
      The table is not correct !! \n\
Do you really want to save the table ? \n,XATReallySaveTable(//),,,Save
notify, Save,Cancel))
make[2]: *** [XaLeap_wcl] Error 1
make[2]: Leaving directory
'/usr/people/jshin/Amber_Files/amber9/src/leap/src/leap'
make[1]: *** [install] Error 2
make[1]: Leaving directory
'/usr/people/jshin/Amber_Files/amber9/src/leap'
make: *** [serial] Error 2
-----------------------------------

Can you recommend anything to get by this error? I feel like I'm almost

Much Thanks,

John Shin

Walter Reed Army Institute of Research
Division of Molecular Pharmacology
Department of Biochemistry
503 Robert Grant Ave.
Silver Spring, MD 20910
Tel: 301-319-9054

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
Of David A. Case
Sent: Friday, December 15, 2006 6:24 PM
To: amber_at_scripps.edu
Subject: Re: AMBER: Error in sysdepend.c?

On Fri, Dec 15, 2006, Shin, John Y CONTRACTOR WRAIR-Wash DC wrote:

>
> I'm trying to compile Amber 9 on an Octane 2 SGI machine running IRIX
> 6.5.25f using gcc 4.0.3, binutils 2.17, and g95 0.9. I use the
> following commands to compile:
>
> 1. ./configure g95

The "g95" target in Amber was never tuned for SGI/MIPS compilation. So,
there may well be incompatibilties. [I know this is pretty well hidden,
but "configure" does say this: g95 or gfortran compiler (Linux/cygwin
only) .]

We are only now hearing from people who have sgi/mips machines but don't
have the sgi compilers. So, there is probably some work to be done.

> sysdepend.c: In function 'SysdependDirectoryList':
> sysdepend.c:177: warning: passing argument 2 of 'BSDscandir' from
> incompatible pointer type
> sysdepend.c:186: error: dereferencing pointer to incomplete type

You will need to add "-DSYSV" to the CFLAGS variable in config.h. More
may be needed, but this will prevent the compiler from thinking you are
on a BSD system.

...good luck...dac

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