1) AmberTools 1.2

   Décompresser le package:
    
     ssh soft@xsnl10f300f.pharma.aventis.com
     
     cd /local/app/amber/

     tar jxvf AmberTools-1.2.tar.bz2

     export AMBERHOME=/local/app/amber/amber10

     cd $AMBERHOME

     [import patch]

     patch -p0 -N < bugfix_ambertools1.2.all | tee bugfix.log

     Edit: "src/gleap/mortsrc/common/fortran.cpp" 

     Add on line 4: #include <cstdio>

     cd /local/app/amber/amber10/src
     
     ./configure_at gcc

     make -f Makefile_at

     [Import "box120.off" created by Jeremy Fidelak]

     cd $AMBERHOME/dat/leap/lib

     cp /source/box120.off .

     [Importer "Amber99SB" modified by Hummer, Best et Piana]

     cd /local/app/amber

     cp /local/app/amber/amber99SB_Hummer_Best_Piana.tar $AMBERHOME/dat/leap/

     tar xvf amber99SB_Hummer_Best_Piana.tar

[soft@xsnl10f300f src]$ ./configure_at gcc
===================================================================================
Setting AMBERHOME to /local/app/amber/amber10

Using Intel MKL libraries in /opt/intel/mkl/10.0.4.023
Warning: the X11 libraries are not in the usual location !
    To search for them try the command: locate libXt
    On Fedora Core 5 install an xorg-x11-devel package.
    On RedHat8 install an XFree86-devel package.
    For the moment Amber will be configured not to build XLEaP.

Testing the C compiler:
      gcc  -m64 -o testp testp.c
OK

Obtaining the C++ compiler version:
      g++ -v
The version is 4.4.6
OK

Testing the g77 compiler:
     g77 -O2 -fno-automatic -finit-local-zero -o testp testp.f
./configure_at: line 538: g77: command not found
./configure_at: line 539: ./testp: No such file or directory
Unable to compile a Fortran program using g77 -O2 -fno-automatic -finit-local-zero

Testing the gfortran compiler:
     gfortran -O1 -fno-automatic -o testp testp.f
OK

Testing flex:
OK

Configuring netcdf; (may be time-consuming)

NETCDF configure succeeded.

The configuration file, config.h, was successfully created.

The next step is to type 'make -f Makefile_at'
====================================================================================

[soft@xsnl10f300f src]$ make -f Makefile_at
====================================================================================
mkdir /local/app/amber/amber10/bin /local/app/amber/amber10/lib /local/app/amber/amber10/include
mkdir: cannot create directory `/local/app/amber/amber10/bin': File exists
mkdir: cannot create directory `/local/app/amber/amber10/lib': File exists
mkdir: cannot create directory `/local/app/amber/amber10/include': File exists
make: [install] Error 1 (ignored)
(cd ucpp-1.3 && make install )
make[1]: Entering directory `/local/app/amber/amber10/src/ucpp-1.3'
Makefile:35: warning: overriding commands for target `.c.o'
../config.h:99: warning: ignoring old commands for target `.c.o'
gcc  -o ucpp mem.o nhash.o cpp.o lexer.o assert.o macro.o eval.o
mv ucpp /local/app/amber/amber10/bin
make[1]: Leaving directory `/local/app/amber/amber10/src/ucpp-1.3'
(cd byacc && make install )
make[1]: Entering directory `/local/app/amber/amber10/src/byacc'
main.o: In function `create_file_names':
main.c:(.text+0x641): warning: the use of `mktemp' is dangerous, better use `mkstemp'
mv yacc /local/app/amber/amber10/bin
make[1]: Leaving directory `/local/app/amber/amber10/src/byacc'
(cd carpack && make install );
make[1]: Entering directory `/local/app/amber/amber10/src/carpack'
Makefile:7: warning: overriding commands for target `.c.o'
../config.h:99: warning: ignoring old commands for target `.c.o'
ar rv arpack.a dgetv0.o dlaqrb.o dnaitr.o dnapps.o dnaup2.o dnaupd.o dnconv.o dneigh.o dneupd.o dngets.o dsaitr.o dsapps.o dsaup2.o dsaupd.o dsconv.o dseigt.o dsesrt.o dseupd.o dsgets.o dsortc.o dsortr.o dstatn.o dstats.o dstqrb.o dsarpack.o wallclock.o dmout.o ivout.o dvout.o
ar: creating arpack.a
a - dgetv0.o
a - dlaqrb.o
a - dnaitr.o
a - dnapps.o
a - dnaup2.o
a - dnaupd.o
a - dnconv.o
a - dneigh.o
a - dneupd.o
a - dngets.o
a - dsaitr.o
a - dsapps.o
a - dsaup2.o
a - dsaupd.o
a - dsconv.o
a - dseigt.o
a - dsesrt.o
a - dseupd.o
a - dsgets.o
a - dsortc.o
a - dsortr.o
a - dstatn.o
a - dstats.o
a - dstqrb.o
a - dsarpack.o
a - wallclock.o
a - dmout.o
a - ivout.o
a - dvout.o
ranlib arpack.a
mv arpack.a /local/app/amber/amber10/lib
make[1]: Leaving directory `/local/app/amber/amber10/src/carpack'
(cd clapack && make skip )
make[1]: Entering directory `/local/app/amber/amber10/src/clapack'
Makefile:7: warning: overriding commands for target `.c.o'
../config.h:99: warning: ignoring old commands for target `.c.o'
skipping compilation of LAPACK
make[1]: Leaving directory `/local/app/amber/amber10/src/clapack'
(cd cblas && make skip )
make[1]: Entering directory `/local/app/amber/amber10/src/cblas'
Makefile:7: warning: overriding commands for target `.c.o'
../config.h:99: warning: ignoring old commands for target `.c.o'
skipping compilation of BLAS
make[1]: Leaving directory `/local/app/amber/amber10/src/cblas'
(cd f2c &&  make install  )
make[1]: Entering directory `/local/app/amber/amber10/src/f2c'
Makefile:7: warning: overriding commands for target `.c.o'
../config.h:99: warning: ignoring old commands for target `.c.o'
ar rv f2c.a abort_.o  d_atan.o  d_cosh.o  d_int.o   d_nint.o  d_sinh.o d_abs.o   d_atn2.o  d_dim.o   d_lg10.o  d_prod.o  d_sqrt.o  exit_.o d_acos.o  d_exp.o   d_log.o   d_sign.o  d_tan.o d_asin.o  d_cos.o   d_mod.o   d_sin.o   d_tanh.o wsfe.o s_cmp.o s_copy.o s_paus.o s_rnge.o s_stop.o wsle.o xwsne.o util.o wref.o wrtfmt.o rsne.o sfe.o sue.o uio.o open.o rdfmt.o rewind.o rsfe.o rsli.o ilnw.o inquire.o lread.o fmtlib.o ftell_.o iio.o err.o close.o dfe.o dolio.o due.o endfile.o backspace.o fmt.o sig_die.o pow_dd.o pow_di.o pow_ii.o lwrite.o i_len.o s_cat.o F77_aloc.o wsne.o typesize.o
ar: creating f2c.a
a - abort_.o
a - d_atan.o
a - d_cosh.o
a - d_int.o
a - d_nint.o
a - d_sinh.o
a - d_abs.o
a - d_atn2.o
a - d_dim.o
a - d_lg10.o
a - d_prod.o
a - d_sqrt.o
a - exit_.o
a - d_acos.o
a - d_exp.o
a - d_log.o
a - d_sign.o
a - d_tan.o
a - d_asin.o
a - d_cos.o
a - d_mod.o
a - d_sin.o
a - d_tanh.o
a - wsfe.o
a - s_cmp.o
a - s_copy.o
a - s_paus.o
a - s_rnge.o
a - s_stop.o
a - wsle.o
a - xwsne.o
a - util.o
a - wref.o
a - wrtfmt.o
a - rsne.o
a - sfe.o
a - sue.o
a - uio.o
a - open.o
a - rdfmt.o
a - rewind.o
a - rsfe.o
a - rsli.o
a - ilnw.o
a - inquire.o
a - lread.o
a - fmtlib.o
a - ftell_.o
a - iio.o
a - err.o
a - close.o
a - dfe.o
a - dolio.o
a - due.o
a - endfile.o
a - backspace.o
a - fmt.o
a - sig_die.o
a - pow_dd.o
a - pow_di.o
a - pow_ii.o
a - lwrite.o
a - i_len.o
a - s_cat.o
a - F77_aloc.o
a - wsne.o
a - typesize.o
ranlib f2c.a
mv f2c.a /local/app/amber/amber10/lib
make[1]: Leaving directory `/local/app/amber/amber10/src/f2c'
(cd c9x-complex && make skip )
make[1]: Entering directory `/local/app/amber/amber10/src/c9x-complex'
using built-in (C99) complex.h functionality
make[1]: Leaving directory `/local/app/amber/amber10/src/c9x-complex'
(cd cifparse && make install )
make[1]: Entering directory `/local/app/amber/amber10/src/cifparse'
Makefile:7: warning: overriding commands for target `.c.o'
../config.h:99: warning: ignoring old commands for target `.c.o'
rm -f cifparse.a
ar rv cifparse.a lex.cif.o cifp.tab.o cifparse.o
ar: creating cifparse.a
a - lex.cif.o
a - cifp.tab.o
a - cifparse.o
ranlib cifparse.a
mv cifparse.a /local/app/amber/amber10/lib
make[1]: Leaving directory `/local/app/amber/amber10/src/cifparse'
(cd nab && make install )
make[1]: Entering directory `/local/app/amber/amber10/src/nab'
./nab  -c -DDATDIR='"/local/app/amber/amber10/dat"'  na_anal.nab
na_anal.c: In function ‘helixanal’:
na_anal.c:2417: error: expected ‘)’ before ‘is’
na_anal.c:2417: error: stray ‘\’ in program
na_anal.c:2417:41: warning: missing terminating " character
na_anal.c:2417: error: missing terminating " character
na_anal.c:2419: error: expected ‘;’ before ‘}’ token
cc failed!
make[1]: *** [na_anal.o] Error 1
make[1]: Leaving directory `/local/app/amber/amber10/src/nab'
make: *** [install] Error 2
======================================================================================

2) Amber 10

   2.1) Serial compilation:

          cd /local/app/amber

          tar xvfj Amber10.tar.bz2

          export AMBERHOME=/local/app/amber/amber10

          cd $AMBERHOME

          [import patch + apply_bugfix_all.x]

          mv bugfix.all bugfix_amber10.all

          ./apply_bugfix_all.x bugfix.all | tee bugfix.log

          cd src

          ./configure_amber -static gfortran

          make serial

          cd ../test

          make test

          [if error] mv TEST_FAILURES.diff TEST_FAILURES.diff.MM

          make test.serial.QMMM
 
          [if error] mv TEST_FAILURES.diff TEST_FAILURES.diff.QMMM

[soft@xsnl10f300f src]$ ./configure_amber -static gfortran
===================================================================================
Setting AMBERHOME to /local/app/amber/amber10

Setting up Amber configuration file for architecture: gfortran
Using parallel communications library: none
The MKL_HOME environment variable is not defined.

Testing the C compiler:
      gcc  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -O2 -m64 -o testp testp.c
OK

Testing the Fortran compiler:
     gfortran -O0 -fno-range-check -fno-second-underscore -o testp testp.f
OK

  ------   Configuring the netCDF libraries:   --------

Configuring netcdf; (may be time-consuming)
configure: WARNING: No F90 compiler found. F90 API will not be built.
configure: error: Could not link conftestf.o and conftest.o
netcdf configure returned 1
NETCDF configure failed!  Check the netcdf_config.log file
====================================================================================

[soft@xsnl10f300f src]$ make serial
====================================================================================
Starting installation of Amber10 (serial) at Tue Oct 16 18:25:36 CEST 2012.
cd lib && make install
make[1]: Entering directory `/local/app/amber/amber10/src/lib'
gfortran     -o new2oldparm new2oldparm.o nxtsec.o
mv new2oldparm ../../exe
/bin/rm _*.f
/bin/rm: cannot remove `_*.f': No such file or directory
make[1]: [install] Error 1 (ignored)
make[1]: Leaving directory `/local/app/amber/amber10/src/lib'
cd addles && make install
make[1]: Entering directory `/local/app/amber/amber10/src/addles'
cd ../lib; ./Makelist ../lib/random.o ../lib/mexit.o  ../lib/nxtsec.o
make[2]: Entering directory `/local/app/amber/amber10/src/lib'
make[2]: `random.o' is up to date.
make[2]: Leaving directory `/local/app/amber/amber10/src/lib'
make[2]: Entering directory `/local/app/amber/amber10/src/lib'
make[2]: `mexit.o' is up to date.
make[2]: Leaving directory `/local/app/amber/amber10/src/lib'
make[2]: Entering directory `/local/app/amber/amber10/src/lib'
make[2]: `nxtsec.o' is up to date.
make[2]: Leaving directory `/local/app/amber/amber10/src/lib'
gfortran     -o addles lesmain.o addspace.o readprm.o writprm.o readcrd.o writcrd.o pick.o       rline.o   nxt.o intgr.o   find.o    of.o geti.o    unit.o    getc.o alert.o   echo.o    get4c.o getd.o    wlesprm.o lesprm.o les2prm.o checksz.o addspace_atm1st.o ../lib/random.o ../lib/mexit.o  ../lib/nxtsec.o -L/opt/intel/mkl/10.0.4.023/lib/em64t -lvml -lmkl_lapack -lmkl -lguide -lpthread
/usr/bin/ld: cannot find -lvml
collect2: ld returned 1 exit status
make[1]: *** [addles] Error 1
make[1]: Leaving directory `/local/app/amber/amber10/src/addles'
make: *** [serial] Error 2
======================================================================================

   
  2.2) Parallel Compilation:

        * Mise en place de sander.MPI:

          make clean

          export MKL_HOME=/opt/intel/mkl/10.0.4.023

          export MPI_HOME=/local/app/share/openmpi/1.2.4

          ./configure_amber -openmpi sgi_altix

          (Doute par rapports aux flags)

        * Mise en place de pmemd.MPI:

          Définir l'environnement:

            cd src/pmemd

            export AMBERHOME=/local/app/amber/amber10

            export MPI_HOME=/local/app/share/openmpi/1.2.4

            export NETCDF_HOME=$AMBERHOME/src/netcdf

          Création des fichiers suivants :

            [soft@cldl06 config_data]$ vi interconnect.openmpi
              ==========================================================
 ==========================================================
              MPI_DEFINES = -DMPI -DSLOW_NONBLOCKING_MPI
              MPI_INCLUDE = -I$(MPI_HOME)/include
              MPI_LIBDIR = $(MPI_HOME)/lib
              MPI_LIBS = -L$(MPI_LIBDIR) -lmpi
              ==========================================================
              (doute par rapport au contenu du fichier)

            [soft@cldl06 config_data]$ vi linux_x86_64.gfortran
              ==========================================================
              DIRFRC_DEFINES = -DDIRFRC_EFS -DDIRFRC_NOVEC
              CPP = /lib/cpp
              CPPFLAGS = -traditional -P
              F90_DEFINES = -DFFTLOADBAL_2PROC
              F90 = mpif90
              MODULE_SUFFIX = mod
              F90FLAGS = -c
              F90_OPT_DBG = -g
              F90_OPT_LO =  -O1
              F90_OPT_MED = -O2
              F90_OPT_HI =  -O3 -fno-range-check -fno-second-underscore
              F90_OPT_DFLT =  $(F90_OPT_HI)
              CC = mpicc
              CFLAGS = -O3 -m64
              LOAD = mpif90
              LOADFLAGS =
              LOADLIBS =
              ==========================================================
              (doute par rapport au nom et au contenu du fichier)


        * Configuration de pmemd:

          -bash-3.1$ cd /local/app/amber/amber10/src/pmemd



export MKL_HOME=/opt/intel/mkl/10.0.4.023

export AMBERHOME=/local/app/amber/amber10

export MPI_HOME=/local/app/share/openmpi/1.2.4

export NETCDF_HOME=$AMBERHOME/src/netcdf

Création des fichiers suivants :

cd /local/app/amber/amber10/src/pmemd/config_data

[soft@cldl06 config_data]$ vi interconnect.openmpi
              ==========================================================
              MPI_DEFINES = -DMPI -DSLOW_NONBLOCKING_MPI
              MPI_INCLUDE = -I$(MPI_HOME)/include
              MPI_LIBDIR = $(MPI_HOME)/lib
              MPI_LIBS = -L$(MPI_LIBDIR) -lmpi
              ==========================================================
              (doute par rapport au contenu du fichier)

[soft@cldl06 config_data]$ vi linux_x86_64.gfortran
              ==========================================================
              DIRFRC_DEFINES = -DDIRFRC_EFS -DDIRFRC_NOVEC
              CPP = /lib/cpp
              CPPFLAGS = -traditional -P
              F90_DEFINES = -DFFTLOADBAL_2PROC
              F90 = mpif90
              MODULE_SUFFIX = mod
              F90FLAGS = -c
              F90_OPT_DBG = -g
              F90_OPT_LO =  -O1
              F90_OPT_MED = -O2
              F90_OPT_HI =  -O3 -fno-range-check -fno-second-underscore
              F90_OPT_DFLT =  $(F90_OPT_HI)
              CC = mpicc
              CFLAGS = -O3 -m64
              LOAD = mpif90
              LOADFLAGS =
              LOADLIBS =
              ==========================================================

[soft@xsnl10f300f pmemd]$ ./configure linux_x86_64 gfortran openmpi pubfft bintraj
File config_data/fft.pubfft being used...
configure assumes netCDF files are in /local/app/amber/amber10/src/netcdf.
File config_data/linux_x86_64.gfortran being used...
File config_data/interconnect.openmpi being used...
configure assumes openmpi files are in /local/app/share/openmpi/1.2.4.
PMEMD Configurate successfully completed.

[soft@xsnl10f300f pmemd]$ make install
cd src && make install
make[1]: Entering directory `/local/app/amber/amber10/src/pmemd/src'
cp /local/app/amber/amber10/src/netcdf/include/*.mod .
cp: cannot stat `/local/app/amber/amber10/src/netcdf/include/*.mod': No such file or directory
make[1]: *** [netcdf.mod] Error 1
make[1]: Leaving directory `/local/app/amber/amber10/src/pmemd/src'
make: *** [install] Error 2