AMBER Archive (2008)

Subject: AMBER: Some Problems With the Installation of Ambertools

From: Manikandan Chandrasekaran (mxchandrasek_at_ualr.edu)
Date: Wed Sep 17 2008 - 18:21:06 CDT

Hi ppl,

We people here at MidSouth Bioinformatics Center at the UALR are trying to install Ambertools 1.2 in Sun Solaris for the past few days. But we are encountering some bugs, which we find hard to fix.

We are not pretty sure whether the bugs are a result of the absence of Fortran g77 or gFortran Compiler, which is been mentioned as some sort of prerequisite in the ambermd.org homepage. What we have instead is a FortranG95 Compiler. We like to install the ambertools using this compiler. What we did was, edited the lines FC=g95(instead of g77) and g77=hasg77(instead of g77=nog77, also we tried substituting 77 with 95) in the config.h file present in the amber10/src. But the bugs didn't get fixed.

The following are the steps based on the installation guidelines, which we followed. Can you please help fix the bugs? The commands have been made bold and the errors have been italicized.
Thanks,
Mani
  Step 1 AMBERHOME=/usr/local/amber10/amber10/;export AMBERHOME PATH=$AMBERHOME/exe:$PATH;export PATH   Step 2 (Italized the problems) cd $AMBERHOME/src ./configure_at gcc Setting AMBERHOME to /usr/local/amber10/amber10  
Testing the C compiler:       gcc  -m32 -o testp testp.c OK  Obtaining the C++ compiler version:       g++ -v The version is 3.4.3 OK  
Testing the g77 compiler:      g77 -O2 -fno-automatic -finit-local-zero -o testp testp.f ./configure_at: g77: not found ./configure_at: ./testp: not found 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 ./configure_at: gfortran: not found ./configure_at: ./testp: not found Unable to compile a Fortran program using gfortran -O1 -fno-automatic We will be unable to compile mopac or resp  Testing flex: OK Configuring netcdf; (may be time-consuming)   NETCDF configure succeeded.   Step 3 make -f Makefile_at   mkdir /usr/local/amber10/amber10/bin /usr/local/amber10/amber10/lib /usr/local/amber10/amber10/include mkdir: Failed to make directory "/usr/local/amber10/amber10/bin"; File exists mkdir: Failed to make directory "/usr/local/amber10/amber10/lib"; File exists mkdir: Failed to make directory "/usr/local/amber10/amber10/include"; File exists *** Error code 2 (ignored)<Whole lot of process/steps>
  mv cifparse.a /usr/local/amber10/amber10/lib (cd nab && make install ) gcc -c -m32 -DBINTRAJ   -o nmode.o nmode.c nmode.c: In function `lnorm': nmode.c:1172: error: `_Imaginary_I' undeclared (first use in this function) nmode.c:1172: error: (Each undeclared identifier is reported only once nmode.c:1172: error: for each function it appears in.) *** Error code 1 make: Fatal error: Command failed for target `nmode.o' Current working directory /usr/local/amber10/amber10/src/nab *** Error code 1 make: Fatal error: Command failed for target `install'   Step 4cd $AMBERHOME/test;  make -f Makefile_at test   ( cd nab; make test ) ===================================================== Running test to make dna duplex:     sh: /usr/local/amber10/amber10/bin/nab: not found *** Error code 1 The following command caused the error: /usr/local/amber10/amber10/bin/nab  -o duplex duplex.nab; \         ./duplex < duplex.in make: Fatal error: Command failed for target `duplex_test' Current working directory /usr/local/amber10/amber10/test/nab *** Error code 1 make: Fatal error: Command failed for target `test.nab'    

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