AMBER Archive (2004)

Subject: Re: AMBER: A question on AMBER8 installation

From: Hwankyu Lee (leehk_at_umich.edu)
Date: Thu Oct 14 2004 - 22:01:05 CDT

Thanks for many kind answers so far. I solved some problems, but still have one.

I realized that I don't have X development system in my fedora2. So, I installed
X development system. Also, I tried both ifort v8.1 and v8.0. I don't see any
different results from both.
When I typed "make test", I got an error, which shows that ./run.tleap failed.
So, I went to the /amber8/src/leap and then type "make install", and could make
**leap files in amber8/exe/.
An then, when I ran "make test" again, I could see that tleap is passed, but got
similar error about antechamber like below.

==============================================================
cd antechamber/tp; ./Run.tp
../../../exe/antechamber: Command not found.
  ./Run.tp: Program error
make: *** [test.antechamber] Error 1

So, I also went to /src/antechamber and then type "make install" like I did for
leap. But, it didn't work for antechamber.
How can I build up antechamber file in /amber8/exe/.

I really appreciate your kind answers, again.

best,
Hwankyu

Quoting "M. L. Dodson" <bdodson_at_scms.utmb.edu>:

> Pardon me for butting in, can you build leap all by itself?
> Leap does not involve any fortran and works just fine with
> gcc/g++. See below.
>
> On Thursday 14 October 2004 12:57 pm, Hwankyu Lee wrote:
> > 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.
> >
> >
>
> The file should be:
> /usr/X11R6/include/X11/Intrinsic.h
>
> Note the exact spelling and be aware that unix file system naming
> is case sensitive.
>
> If you really mean there is no file there (i.e., the directory is
> empty), you probably need to install the X development system
> (rpm? I don't normally do Linux.) If you just mean that intrinsic.h is
> not there, then it is because you are ignoring the capitalization
> of the Intrinsic.h file name.
>
> If leap now builds correctly, pardon my intrusion. I have no
> useful comments on the ins and outs of Intel compilers, I just use
> ifc version 7 and live with the performance hit.
>
> Bud Dodson
>
> >
> > Quoting Ross Walker <ross_at_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_at_rosswalker.co.uk |
> > > | http://www.rosswalker.co.uk/ | PGP Key available on request |
>
>
> --
> M. L. Dodson bdodson_at_scms.utmb.edu
> 409-772-2178 FAX: 409-747-8608
>
>
>
>
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>

------------------------------------------------------
Hwankyu Lee.

Graduate student research assistant, The Larson group.
Department of Biomedical Engineering.
University of Michigan - Ann Arbor.
Email: leehk_at_umich.edu, hklee910_at_hotmail.com
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