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--- > fc="gfortran -fno-automatic" 439,440c439,440 < fc=g77 < echo "Mopac and resp will be compiled with g77" --- > fc=gfortran -fno-automatic > echo "Mopac and resp will be compiled with gfortran" 442c442 < fflags="-O0" --- > fflags="-O1" When I ran make -f Makefile_at test all of the tests in the ncsu directory failed with an error that looked like this: > ** NCSU-Error ** : expected list value for key 'i', got '<EMPTY>' instead --------------------------------------- possible FAILURE: check pmd.txt.dif /extra/p530/software/amber10/test/ncsu/pmd Other than that the antechamber tests failed with errors like: /extra/p530/software/amber10/test/antechamber/fluorescein 8c8 < 2 C2 1.9170 3.7710 0.1310 ca 1 FLR 0.591300 > 2 C2 1.9170 3.7710 0.1310 ca 1 FLR 0.589100 -Sam On Fri, May 16, 2008 at 10:41 AM, Sam Danziger <sam.danziger.gmail.com> wrote: > 4.3.0 update: > > I checked the lib directory and found that the copy of > libpdb.a > was two days old, although all of the other .a's were recently regenerated. > > I deleted libpdb.a and then reran make -f Makefile_at. > > It looks like Amber Tools compiled and installed correctly after that, > although this is without any of the fortran parts as 4.3.0 does not > include g77. > > -Sam > > On Fri, May 16, 2008 at 10:06 AM, Sam Danziger <sam.danziger.gmail.com> wrote: >> David, >> >> Thanks for the response, I was starting to fear that my problem had >> dissapeared into the great beyond. >> >> Here is the gcc 4.3.0 error message. Note: I had to change to >> gfortran and not compile mopac to get this far. >> >> Thank you, >> -Sam >> >> gcc -o rdparm main.o rdparm.o dispatch.o help.o utility.o second.o io.o trajecto >> ry.o evec.o torsion.o mask.o rms.o display.o interface.o energy.o experimental.o >> ptraj.o actions.o analyze.o thermo.o pubfft.o cluster.o clusterLib.o /extra/p53 >> 0/software/amber10/lib/libpdb.a /extra/p530/software/amber10/lib/libsym.a /extra >> /p530/software/amber10/lib/arpack.a /extra/p530/software/amber10/lib/lapack.a /e >> xtra/p530/software/amber10/lib/blas.a /extra/p530/software/amber10/lib/f2c.a >> ../netcdf/lib/libnetcdf.a -lm >> /extra/p530/software/amber10/lib/libpdb.a(pdb_read.o): In function `pdb_read_str >> ing.': >> pdb_read.c:(.text+0x1d32): undefined reference to `_intel_fast_memset' >> /extra/p530/software/amber10/lib/libpdb.a(pdb_sscanf.o): In function `pdb_sscanf >> ': >> pdb_sscanf.c:(.text+0x2a0): undefined reference to `_intel_fast_memset' >> /extra/p530/software/amber10/lib/libpdb.a(pdb_sprntf.o): In function `pdb_sprint >> f': >> pdb_sprntf.c:(.text+0x2b9): undefined reference to `_intel_fast_memset' >> pdb_sprntf.c:(.text+0x4de): undefined reference to `_intel_fast_memset' >> pdb_sprntf.c:(.text+0x7ea): undefined reference to `_intel_fast_memset' >> /extra/p530/software/amber10/lib/libpdb.a(pdb_sprntf.o): In function `outexp': >> pdb_sprntf.c:(.text+0xbab): undefined reference to `__intel_f2int' >> pdb_sprntf.c:(.text+0xbd7): undefined reference to `__intel_f2int' >> pdb_sprntf.c:(.text+0xd4a): undefined reference to `_intel_fast_memset' >> /extra/p530/software/amber10/lib/libpdb.a(pdb_sprntf.o): In function `outfloat': >> >> pdb_sprntf.c:(.text+0xdd7): undefined reference to `__intel_f2int' >> pdb_sprntf.c:(.text+0xe09): undefined reference to `_intel_fast_memset' >> pdb_sprntf.c:(.text+0xf91): undefined reference to `_intel_fast_memcpy' >> pdb_sprntf.c:(.text+0x100d): undefined reference to `_intel_fast_memset' >> pdb_sprntf.c:(.text+0x1033): undefined reference to `_intel_fast_memset' >> /extra/p530/software/amber10/lib/libpdb.a(pdb_sprntf.o): In function `outstr': >> pdb_sprntf.c:(.text+0x1151): undefined reference to `_intel_fast_memcpy' >> pdb_sprntf.c:(.text+0x119b): undefined reference to `_intel_fast_memset' >> /extra/p530/software/amber10/lib/libpdb.a(pdb_sprntf.o): In function `outunsigne >> d': >> pdb_sprntf.c:(.text+0x12a7): undefined reference to `_intel_fast_memset' >> /extra/p530/software/amber10/lib/libpdb.a(pdb_sprntf.o): In function `outint': >> pdb_sprntf.c:(.text+0x13f7): undefined reference to `_intel_fast_memset' >> collect2: ld returned 1 exit status >> make[1]: *** [rdparm] Error 1 >> make[1]: Leaving directory `/extra/p530/software/amber10/src/ptraj' >> make: *** [install] Error 2 >> >> >> On Thu, May 15, 2008 at 9:47 PM, David A. Case <case.scripps.edu> wrote: >>> On Mon, May 12, 2008, Sam Danziger wrote: >>> >>>> I've tried to install Amber Tools 1.0, but get an error message when I >>>> try to compile. >>>> >>>> I'm using Gentoo linux (Linux version 2.6.22-gentoo-r18), and have >>>> tried gcc 3.4.1, 3.4.4 and 4.3.0 (4.3.0 gives me a different error >>>> than below). >>>> >>> >>> Thanks for the report; aren't C++ error messages awe-inspiring sometimes? >>> >>> I've entered this into bugzilla. Probably no developer has used Gentoo, >>> although other Linux and Mac and cygwin versions of gcc seem OK here. >>> >>> It might be helpful to post the 4.3.0 error message as well...you never know >>> when a clue will pop up. >>> >>> ...regards...dac >>> >>> ----------------------------------------------------------------------- >>> The AMBER Mail Reflector >>> To post, send mail to amber.scripps.edu >>> To unsubscribe, send "unsubscribe amber" (in the *body* of the email) >>> to majordomo.scripps.edu >>> >> >> >> >> -- >> Samuel A. Danziger >> Dept. of Biomedical Engineering >> PhD Candidate >> University of California >> Irvine, CA 92697 >> sdanzige.uci.edu >> (908)246-4502 >> http://samdanziger.com/ >> >> Associated Graduate Students >> VP Financial Affairs >> vpfinance.ags.uci.edu >> >> Truth Cannot Contradict Truth >> > > > > -- > Samuel A. Danziger > Dept. of Biomedical Engineering > PhD Candidate > University of California > Irvine, CA 92697 > sdanzige.uci.edu > (908)246-4502 > http://samdanziger.com/ > > Associated Graduate Students > VP Financial Affairs > vpfinance.ags.uci.edu > > Truth Cannot Contradict Truth > -- Samuel A. Danziger Dept. of Biomedical Engineering PhD Candidate University of California Irvine, CA 92697 sdanzige.uci.edu (908)246-4502 http://samdanziger.com/ Associated Graduate Students VP Financial Affairs vpfinance.ags.uci.edu Truth Cannot Contradict Truth ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber.scripps.edu To unsubscribe, send "unsubscribe amber" (in the *body* of the email) to majordomo.scripps.eduReceived on Sun May 18 2008 - 06:07:51 PDT