I want to add one more thing to the last post (below).
when I did "make clean", I also got some errors like below.
-----------------
make[2]: [clean] Error 1 (ignored)
/bin/rm XaLeap_wcl
/bin/rm: cannot remove `XaLeap_wcl': No such file or directory
make[2]: [clean] Error 1 (ignored)
/bin/rm *.gprof
/bin/rm: cannot remove `*.gprof': No such file or directory
------------------
Quoting Hwankyu Lee <leehk.umich.edu>:
> I appreciate your answers..but, still have problems..
> I exactly followed Ross's procedures...I started all the procedures from the
> top.
> 1)tar xvf AMBER8.tar
> 2)cd /home/leehk/local/amber8
> setenv AMBERHOME /home/leehk/local/amber8
> 3)cd home/leehk/local/amber8/
> patch -p0 -N -r patch_rejects <bugfix.all (going well)
> 4)cd home/leehk/local/amber8/src
> setenv MKL_HOME /opt/intel/mkl70
> 5)cd /leehk/local/amber8/src
> ./configure -p4 -static -nopar ifort
> 6)Edit config.h and change gcc and g++ to icc
> 7)make clean
> 8)make or make serial
> 9)cd /leehk/local/amber8/test
> make test
>
> AFter 8), I have error like this at the end of execution.
> --------------
>
bondtype.o(.gnu.linkonce.t._ZSt24__uninitialized_copy_auxIN9__gnu_cxx17__normal_iteratorIP5PointSt6vectorIS2_SaIS2_EEEES7_ET0_T_S9_S8_12__false_type+0x91):
> In function `destr_detour20.0.156':
> : undefined reference to `__cxa_end_catch'
> bondtype.o(.eh_frame+0x12): In function `.eh_frame_seg':
> : undefined reference to `__gxx_personality_v0'
> make[1]: *** [bondtype] Error 1
> make[1]: Leaving directory `/home/leehk/local/amber8/src/antechamber'
> make: *** [serial] Error 2
> -----------------
>
> After 9), I have this error.
> -----------------
> cd dmp; ./Run.dmp
> diffing mdout.dmp.save with mdout.dmp
> PASSED
> ==============================================================
> cd adenine; ./Run.adenine
> diffing mdout.adenine.save with mdout.adenine
> PASSED
> ==============================================================
> cd cytosine; ./Run.cytosine
> Badly placed ()'s.
> make: *** [test.sander.no_lmod] Error 1
> --------------------
>
> In terms of intrinsic.h file, I couldn't find the file. In
> /usr/X11R6/include,
> thers is no file there. I'm using fedora 2.
> Could you give me other hints for this problem, please?
> Thanks for you help.
>
> best,
> Hwankyu.
>
>
>
> Quoting Ross Walker <ross.rosswalker.co.uk>:
>
> > Dear Hwankyu,
> >
> > > ./configure -p4 -nopar -ifort
> >
> > You definitely did ./configure -p4 -nopar ifort here yes (I.e no - before
> > the ifort)?
> >
> > > icc -c -O2 -o makeDIST_RST.o makeDIST_RST.c
> > > makeDIST_RST.c(338): warning #266: function declared implicitly
> > > if ( !lookuprtyp(atma.rnum,atma.nrtyp) ||
> >
> > Don't worry about these. They are just warnings. The compiler thinks the
> > routines are declared implicitly because the call to the routine comes
> > earlier in the file than the actual routine and the function is not
> > prototyped at the beginning of the file. This occurs because icc is not
> > really smart enough to scan through the file twice before reporting
> > warnings. This sort of error is only a problem if it occurs at the link
> > stage (when all routines must have been declared in the object files or
> > libraries).
> >
> > > bondtype.o(.eh_frame+0x12): undefined reference to
> > > `__gxx_personality_v0'
> >
> > Are you certain you did:
> >
> > cd $AMBERHOME/src/
> > make clean
> >
> > Before you did the make?
> >
> > The reason I ask is because the __ in front of gxx_peronality_v0 looks like
> > the naming convention used by gcc. As far as I am aware icc only expects
> one
> > underscore. Hence it looks like all the object files were not cleaned from
> > the directory before you ran the make again.
> >
> > If you have not done it, I would suggest the following:
> >
> > Remove your existing amber8 directory tree.
> >
> > 1) Get hold of the original tar file from the amber8 cd (so you know it is
> > unmodified).
> > 2) Untar this to a folder on your machine.
> > 3) set AMBERHOME to this directory setenv AMBERHOME /path_to_inst/amber8
> > 3) Obtain the latest bugfixes from here:
> > http://amber.scripps.edu/bugfixes/8.0/bugfix.all - save it in the amber8
> > directory the untaring created.
> > 4) Patch your amber8 copy with these bugfixes:
> > cd $AMBERHOME
> > patch -p0 -N -r patch_rejects < bugfix.all
> > 5) cd into the src directory
> > cd $AMBERHOME/src
> > 6) Create the configure script
> > ./configure -p4 -static -nopar ifort
> > 7) Edit config.h and change all gcc and g++ to icc
> > 8) clean everything
> > make clean
> > 9) make
> > 10) cd $AMBEROME/test
> > 11) make
> >
> > See how you get on. The important thing is to make sure you are starting
> > from a clean un-aulterated copy of amber8.
> >
> > All the best
> > Ross
> >
> >
> > /\
> > \/
> > |\oss Walker
> >
> > | Department of Molecular Biology TPC15 |
> > | The Scripps Research Institute |
> > | Tel:- +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
> > | http://www.rosswalker.co.uk/ | PGP Key available on request |
> >
> > -----------------------------------------------------------------------
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> >
> >
> >
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>
>
>
------------------------------------------------------
Hwankyu Lee.
Graduate student research assistant, The Larson group.
Department of Biomedical Engineering.
University of Michigan - Ann Arbor.
Email: leehk.umich.edu, hklee910.hotmail.com
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Received on Thu Oct 14 2004 - 19:53:00 PDT
