AMBER Archive (2004)

Subject: RE: AMBER: A question on AMBER8 installation

From: Hwankyu Lee (leehk_at_umich.edu)
Date: Thu Oct 14 2004 - 12:57:45 CDT

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_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 |
>
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