AMBER Archive (2005)

Subject: AMBER: Installation problem

From: Sukjoon Yoon (yoonsj_at_sookmyung.ac.kr)
Date: Sun Jun 12 2005 - 23:07:26 CDT

Dear Chris and Users,

I tried various ways to install AMBER 8 on my machine. Any comments and
helpful hints will be appreciated. I attahced the detail here. When I
tried "./configure ifort" and "make serial", a lot of warning message
appeared and ended up with an Error message.

Thanks,

Sukjoon

Machine: Xeon dual process, Fedore Core 3 x86_64 installed.

glibc-2.3.5.....i386.rpm
glibc-common-2.3.5.....i386.rpm
glibc-devel-2.3.5.....i386.rpm These are additionally
installed for 32bit compile.

************************************************************************
************************************************************************
****

1)

> ./configure ia64_ifort
> make serial
.....................
.....................
icc -c -O2 -o mmtsb_client.o mmtsb_client.c
make[1]: icc: Command not found
make[1]: *** [mmtsb_client.o] Error 127
make[1]: Leaving directory `/opt/amber8/src/sander'
make: *** [serial] Error 2

2)

> ./configure ifort
> make serial
.....................
.....................
pdbFile.c:1821: warning: initialization from incompatible pointer type
....................
xaUnitEditor.c:282: warning: cast to pointer from integer of different
size
....................
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 XrawRegistr.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
/usr/bin/ld: cannot find -lXt
collect2: ld returned 1 exit status
make[2]: *** [xaLeap] Error 1
make[2]: Leaving directory `/opt/amber8/src/leap/src/leap'
make[1]: *** [install] Error 2
make[1]: Leaving directory `/opt/amber8/src/leap'
make: *** [serial] Error 2

************************************************************************
************************************************************************
*

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
Of Chris Harrison
Sent: Monday, June 13, 2005 8:04 AM
To: amber_at_scripps.edu
Subject: Re: AMBER: Installation problem

ld: skipping incompatible /usr/lib64/libm.so when searching for -lm
ld: skipping incompatible /usr/lib64/libm.a when searching for -lm
ld: cannot find -lm

Perhaps you have 64 bit libraries installed (lib64) and are attempting a
32bit compile . . . ? Check if you have /usr/lib/libm.so . . . if so,
redirect to these. If not you may need to insure that your glibc
package was installed from a package NOT containing "x86_64" (ie
glibc-2.3.4-2.fc3.x86_64.rpm) but from an i386/i586/i686 package (ie
glibc-2.3.4-2.fc3.i686.rpm).

chris

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