AMBER Archive (2009)

Subject: RE: [AMBER] AmberTools compiling error

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Sun Apr 26 2009 - 20:55:06 CDT

Hi Farly,

This looks like either something went wrong during the netcdf library build
or the AMBERTools tree you have was not clean when you started building and
netcdf was already built with a different compiler.

You could try:

cd $AMBERHOME
make -f Makefile_at clean
make -f Makefile_at

and see if it builds the second time.

Alternatively as a workaround you could try building without netcdf support.
Make clean as above and then run ./configure_at again and add the flag
-nobintraj.

All the best
Ross

> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf Of Farly Walsh
> Sent: Sunday, April 26, 2009 5:41 PM
> To: amber_at_ambermd.org
> Subject: [AMBER] AmberTools compiling error
>
> HI all!
>
> May be somebody got the same error after running "make -f Makefile_at":
>
> sed -e "s?BINDIR?/home/lparsons/build_amber/bin?" mopac.sh >
> /home/lparsons/build_amber/bin/mopac.sh
> chmod +x /home/lparsons/build_amber/bin/mopac.sh
> mv -f am1bcc acdoctor antechamber atomtype bondtype charmmgen database
> espgen parmcal parmchk prepgen residuegen respgen translate top2mol2
> /home/lparsons/build_amber/bin
> make[1]: Leaving directory `/home/lparsons/build_amber/src/antechamber'
> (cd mopac6/src && make hasG77 )
> make[1]: Entering directory `/home/lparsons/build_amber/src/mopac6/src'
> g77 aababc.o readmo.o writmo.o mopac.o analyt.o anavib.o axis.o
> block.o bonds.o brlzon.o calpar.o capcor.o cdiag.o chrge.o cnvg.o
> compfg.o datin.o dcart.o delmol.o delri.o denrot.o densit.o
> depvar.o deri0.o deri1.o deri2.o deri21.o deri22.o deri23.o
> deritr.o deriv.o dernvo.o ders.o dfock2.o dfpsav.o diag.o diat.o
> diat2.o diis.o dijkl1.o dijkl2.o dipind.o dipole.o dofs.o dot.o
> drc.o drcout.o ef.o enpart.o exchng.o ffhpol.o flepo.o fmat.o
> fock1.o fock2.o force.o formxy.o forsav.o frame.o freqcy.o
> geout.o
> geoutg.o getgeg.o getgeo.o getsym.o gettxt.o gmetry.o gover.o
> grid.o h1elec.o haddon.o hcore.o helect.o hqrii.o ijkl.o interp.o
> iter.o jcarin.o linmin.o local.o locmin.o mamult.o matout.o
> matpak.o meci.o mecid.o mecih.o mecip.o moldat.o molval.o
> mullik.o
> mult.o nllsq.o nuchar.o parsav.o partxy.o pathk.o paths.o perm.o
> polar.o powsav.o powsq.o prtdrc.o quadr.o react1.o reada.o
> refer.o
> repp.o rotat.o rotate.o rsp.o search.o second.o setupg.o solrot.o
> swap.o symtry.o thermo.o timer.o update.o vecprt.o wrtkey.o
> wrttxt.o xyzint.o -o mopac
> mv mopac /home/lparsons/build_amber/bin
> make[1]: Leaving directory `/home/lparsons/build_amber/src/mopac6/src'
> (cd resp && make hasG77 )
> make[1]: Entering directory `/home/lparsons/build_amber/src/resp'
> g77 lapack.o resp.o -o resp
> mv resp /home/lparsons/build_amber/bin
> make[1]: Leaving directory `/home/lparsons/build_amber/src/resp'
> (cd ptraj && make install )
> make[1]: Entering directory `/home/lparsons/build_amber/src/ptraj'
> Makefile:24: warning: overriding commands for target `.c.o'
> ../config.h:99: warning: ignoring old commands for target `.c.o'
> gcc -o rdparm main.o rdparm.o dispatch.o help.o utility.o second.o
> io.o
> trajectory.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 /home/lparsons/build_amber/lib/libpdb.a
> /home/lparsons/build_amber/lib/libsym.a
> /home/lparsons/build_amber/lib/arpack.a
> /home/lparsons/build_amber/lib/lapack.a
> /home/lparsons/build_amber/lib/blas.a
> /home/lparsons/build_amber/lib/f2c.a ../netcdf/lib/libnetcdf.a -lm
> ptraj.o: In function `checkCoordinates':
> ptraj.c:(.text+0x7115): undefined reference to `netcdfGetAttributeText'
> ptraj.c:(.text+0x713b): undefined reference to `netcdfGetAttributeText'
> ptraj.c:(.text+0x7161): undefined reference to `netcdfGetAttributeText'
> ptraj.c:(.text+0x718a): undefined reference to `netcdfGetAttributeText'
> ptraj.c:(.text+0x71b3): undefined reference to `netcdfGetAttributeText'
> ptraj.o:ptraj.c:(.text+0x71d9): more undefined references to
> `netcdfGetAttributeText' follow
> ptraj.o: In function `checkCoordinates':
> ptraj.c:(.text+0x7270): undefined reference to `netcdfGetDimensionInfo'
> ptraj.c:(.text+0x7296): undefined reference to `netcdfGetDimensionInfo'
> ptraj.c:(.text+0x72bc): undefined reference to `netcdfGetDimensionInfo'
> ptraj.o: In function `ptrajOutputCoordinates':
> ptraj.c:(.text+0xf2d0): undefined reference to `netcdfPutAttributeText'
> ptraj.c:(.text+0xf2f3): undefined reference to `netcdfPutAttributeText'
> ptraj.c:(.text+0xf319): undefined reference to `netcdfPutAttributeText'
> ptraj.c:(.text+0xf33f): undefined reference to `netcdfPutAttributeText'
> ptraj.c:(.text+0xf35c): undefined reference to `netcdfPutAttributeText'
> ptraj.o:ptraj.c:(.text+0xf379): more undefined references to
> `netcdfPutAttributeText' follow
> collect2: ld returned 1 exit status
> make[1]: *** [rdparm] Error 1
> make[1]: Leaving directory `/home/lparsons/build_amber/src/ptraj'
> make: *** [install] Error 2
>
>
> I hope that you can help me guys. I am really stuck with this problem.
>
> Thank you,
>
> Farly
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> AMBER_at_ambermd.org
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