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---- Finished with the install of LEaP make[1]: Leaving directory `/theo1/tmp/amber8/src/leap' Installation of Amber8 (serial) is complete at Sun Jul 11 13:55:06 KST 2004. --- ----- Original Message ----- From: "Mark Williamson" <mark.williamson.imperial.ac.uk> To: <amber.scripps.edu> Sent: Sunday, July 11, 2004 2:54 AM Subject: Re: AMBER: Problem amber8 compilation in Opteron(Linux) with PGI-workstation compiler > Jiten wrote: > > > PGC/x86-64 Linux/x86-64 5.1-6: compilation completed with warnings > > /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libXt.so when > > searching for -lXt > > /usr/bin/ld: cannot find -lXt > > make[2]: *** [xaLeap] Error 2 > > make[1]: *** [install] Error 2 > > make: *** [serial] Error 2 > > I think this *may* be caused because /usr/X11R6/lib/libXt.so is a 32bit > library and ld is not going to link a 64bit binary(ies) against it. I > suggest compiling libXt.so as a 64bit library. > Basically a library is a binary which provides a common and often used > functions to other programs. Instead of re-inventing the wheel, > programmers often create libraries that carry out common/repeated tasks > so that other programmers utilise those functions via linking instead of > rewriting their own implementation of them. > > I'm using RHEL WS-3 AMD64 and it has both 32 and 64bit RPMs for > libXt.so, hence it puts the 64bit version of libXt.so in the following > location: > > [root.e01 src]# rpm -ql XFree86-libs-4.3.0-62.EL | grep libXt.so > /usr/X11R6/lib64/libXt.so.6 (this is a symbolic link to the next file) > /usr/X11R6/lib64/libXt.so.6.0 > > and checking that it is actually a 64bit object: > > [root.e01 src]# file /usr/X11R6/lib64/libXt.so.6.0 > /usr/X11R6/lib64/libXt.so.6.0: ELF 64-bit LSB shared object, AMD x86-64, > version 1 (SYSV), stripped > > > I had similar issues, but not identical issues to you. My initial error > when I tried to compile was as follows: > > pgcc -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 <---------------------- > make[2]: *** [xaLeap] Error 2 > make[2]: Leaving directory `/tmp/amber8.14/src/leap/src/leap' > make[1]: *** [install] Error 2 > make[1]: Leaving directory `/tmp/amber8.14/src/leap' > make: *** [serial] Error 2 > > > Ok...so this suggested to me that pgcc could not find the Xt lib when > doing its final link stage. The "-L/usr/X11R6/lib" tells pgcc to look in > this dir for the libraries to link to. I need to tell it to look in > /usr/X11R6/lib64/ , the location of my 64 library. So... how do tell the > build process to this? Well, I searched all the source for a known; in > this cause it was "/usr/X11R6/lib"; > > [root.e01 src]# pwd > /tmp/amber8.14/src > > [root.e01 src]# find ./ | xargs grep "/usr/X11R6/lib" > ../leap/src/leap/Makefile:#/usr/X11R6/lib/libX11.a(XlcDL.o): In function > `try_both_dlsym': > > In this case, I was lucky.. I did not match was I needed exactly, but it > was in the same file; ./leap/src/leap/Makefile > The important part as far as we're concerned is: > > XALEAP_LIB = ../Xraw/libXaw.a ../Wc/libWcLeap.a ../Xpm/libXpm.a \ > ../Xmu/libXmu.a -L$(XHOME)/lib -lXt -lXext -lSM -lICE -lX11 -lm > -lpthread > > My solution was a bit of a dirty hack; addition of a " > -L/usr/X11R6/lib64" to the leap Makefile. > > > XALEAP_LIB = ../Xraw/libXaw.a ../Wc/libWcLeap.a ../Xpm/libXpm.a \ > ../Xmu/libXmu.a -L$(XHOME)/lib -L/usr/X11R6/lib64 -lXt -lXext > -lSM -lICE -lX11 -lm -lpthread > > > Running make again from the root src, produced a complete build. > > > > > cd dmp; ./Run.dmp > > ../Run.dmp: Program error > > I also got this error. Looking further into the actual cause of the > "make test" failure; mdout.dmp: > > > Energy minimization: > maxcyc = 5, ncyc = 10, ntmin = 1 > dx0 = 0.00010, drms = 0.00010 > > Polarizable options: > indmeth = 1, maxiter = 20, irstdip = 0, scaldip = > 0 > diptau = 11.00000, dipmass = 0.33000 > ASSERTion 'ier == 0' failed in extra_pts.f at line 223. > > Looking at the reference file; ./src/sander/extra_pts.f around line 223 > > maxa = max(max11,max12,max13,max14) > allocate( s3(maxa), stat=ier ) > REQUIRE( ier == 0 ) > > It seems that this is somekind of program sanity check and that the > "make test" has failed at this point because integer "ier" is NOT > actually zero at this point. I think that this is the return value from > the allocate() function on the previous line. I'm also assuming "ier" > stands for "Integer Error"; i.e. in C speak, "a return value". When > functions work correctly, it is convention for a function to return a > value of 0 (zero). > > Hence the issue probably lies with "allocate( s3(maxa), stat=ier )". > > > This is where I am now, my current knowledge of fortran/Amber8 internals > is insufficient to solve this one.... > > regards, > > Mark Williamson > http://dumb.ch.ic.ac.uk/~mjw99/ > > > ----------------------------------------------------------------------- > The AMBER Mail Reflector > To post, send mail to amber.scripps.edu > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu > > ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber.scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo.scripps.eduReceived on Sun Jul 11 2004 - 06:53:00 PDT