AMBER Archive (2004)

Subject: RE: AMBER: A question on AMBER8 installation

From: Hwankyu Lee (leehk_at_umich.edu)
Date: Thu Oct 14 2004 - 11:04:18 CDT

Thanks for your advice, but I still have problems.
I followed all the options, and then when I tried option2 (icc instead of
gcc,g++), all the WcCreate.h and WcActCB errors disappeared.
What I did is...
setenv AMBERHOME /home/***/amber8
setenv MKL_HOME /opt/intel/mkl70
cd $AMBERHOME/src
./configure -p4 -nopar -ifort
make or make serial
and then I got this error at the middle and end of execution of make.
-------------------
make[2]: Entering directory `/home/leehk/local/amber8/src/nmr_aux/prepare_input'
/bin/rm *.o _*.f makeDIST_RST makeANG_RST makeSHF.cp makeCHIR_RST.cp \
        makeDIP_RST.protein.cp makeDIP_RST.dna.cp
/bin/rm: cannot remove `_*.f': No such file or directory
/bin/rm: cannot remove `makeDIST_RST': No such file or directory
/bin/rm: cannot remove `makeANG_RST': No such file or directory
/bin/rm: cannot remove `makeSHF.cp': No such file or directory
/bin/rm: cannot remove `makeCHIR_RST.cp': No such file or directory
/bin/rm: cannot remove `makeDIP_RST.protein.cp': No such file or directory
/bin/rm: cannot remove `makeDIP_RST.dna.cp': No such file or directory
make[2]: [clean] Error 1 (ignored)
make[2]: Leaving directory `/home/leehk/local/amber8/src/nmr_aux/prepare_input'
make[2]: Entering directory `/home/leehk/local/amber8/src/nmr_aux/prepare_input'
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) ||
              ^
makeDIST_RST.c(345): warning #266: function declared implicitly
        if ((mapa=mapdefinition(atma.atyp,atma.rtyp))<0){
                  ^
makeDIST_RST.c(350): warning #266: function declared implicitly
        if ((mapb=mapdefinition(atmb.atyp,atmb.rtyp))<0){
.
.
.
bondtype.o(.eh_frame+0x12): 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
--------------------

I used ifort version8.1(l_fc_p_8.018), icc 8.1(l_cc_p_8.1.021), mkl70,
Xorg-x11-6.7.0. When I tried ifrot version 8.0 (l_fc_p_8.0.034), same thing
happens. Could you help me solve this problem, please?

best,
Hwankyu.

Quoting Ross Walker <ross_at_rosswalker.co.uk>:

> Dear Hwanyu,
>
> > got a lot of errors like below (WcCreate.h errors and then
> > WcActCB errors).
> > In file included from WcCreateP.h:19,
> > from WcActCB.c:30:
> > WcCreate.h:225: warning: parameter names (without types) in
> > function declaration
>
> Ok, I have tried this out with a vanilla copy of Amber8 on a similar vanilla
> copy of Fedora Core 2 (Intel P4 2.8, HT on, 1GB) with the following
> compilers and options:
>
> Option 1
> --------
> ifort version 8.0.046 (if you are using an earlier version than this I
> suggest you upgrade as the early release intel 8.0 compilers had a lot of
> bugs), gcc version 3.2.2 20030222, glibc 2.3.2-27.9.7, mkl-6.1
> Xorg-x11-devel-6.7.0-2
>
> setenv AMBERHOME /scratch1/amber8
> setenv MKL_HOME /opt/intel/mkl-6.1
> cd $AMBERHOME/src/
> ./configure -p4 -static -nopar ifort
> make
> make test
>
> This compiles fine and all the tests pass.
>
> Option 2
> --------
> Edit config.h created by configure and change all occurances of gcc and g++
> to icc so that it uses the intel c compiler:
>
> icc version 8.0.066 - Build 20040412Z
>
> This works fine as well.
>
> Option 3
> --------
> Run yum update on the fedora core 2 box to update everything to the latest
> version as of 13th October 2004.
>
> ifort version 8.0.046, gcc version 3.3.3 20040412, glibc 2.3.3-27, mkl-6.1
> Xorg-x11-devel-6.7.0-9
>
> setenv AMBERHOME /scratch1/amber8
> setenv MKL_HOME /opt/intel/mkl-6.1
> cd $AMBERHOME/src/
> ./configure -p4 -static -nopar ifort
> make
> make test
>
> This works fine as well.
>
> Note: I have not tried ifort8.1 since as far as I can tell this only
> supports the 64 bit extended processors to which I do not have access at the
> moment.
>
> 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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