Re: [AMBER] Conflict between AmberTools 1.5 and Cuda

From: Adam Jion <>
Date: Fri, 23 Mar 2012 10:09:32 -0700 (PDT)


When I compile AmberTools 1.5 using gcc-4.6.1 under Ubuntu, it works fine.
However, when I compile using gcc-4.4.6, I get the error of : /usr/bin/ld: cannot find -lgfortran
The full error log is given below.


Error log:

adam.adam-MS-7750:~/amber11/AmberTools/src$ ./configure gnu
Could not find the X11 libraries; you may need to edit config.h
   to set the XHOME and XLIBS variables.
Warning: the X11 libraries are not in the usual location !
    To search for them try the command: locate libXt
    On new Fedora OS's install the libXt-devel libXext-devel
    libX11-devel libICE-devel libSM-devel packages.
    On old Fedora OS's install the xorg-x11-devel package.
    On RedHat OS's install the XFree86-devel package.
    On Ubuntu OS's install the xorg-dev package.
    For the moment Amber will be configured not to build XLEaP.

Obtaining the gnu suite version:
      gcc -v
The version is 4.4.6

Testing the gcc compiler:
     gcc  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -o testp testp.c

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

Testing the gfortran compiler:
     gfortran  -O0 -o testp testp.f

Testing mixed C/Fortran compilation:
     gcc  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE  -c -o testp.c.o testp.c
     gfortran  -O0 -c -o testp.f.o testp.f
     gcc  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c.o testp.f.o -lgfortran
/usr/bin/ld: cannot find -lgfortran
collect2: ld returned 1 exit status
./configure: 1874: ./testp: not found
Error: Unable to compile mixed C/Fortran code.
    Please check your compiler settings and configure flags.

 From: Ross Walker <>
To: 'Adam Jion' <>; 'AMBER Mailing List' <>
Sent: Saturday, March 24, 2012 12:19 AM
Subject: Re: [AMBER] Conflict between AmberTools 1.5 and Cuda
Hi Adam,

> I have a conflict between AmberTools 1.5 and Cuda
> AmberTools 1.5 requires at least a gcc 4.6 and above.
> But the Cuda ToolKit requires a gcc 4.4 and below.
> How do I reconcile the two?

You don't need to build AmberTools in order to build the cuda executables.
You just need to have AmberTools 1.5 extracted in the AMBER directory. Where
are you finding the gcc 4.6 requirement btw? - I have no issues building all
of AMBER 11 and AmberTools 1.5 using RedHat 6 and GCC 4.4.6 and NVCC 4.0.

All the best

|\oss Walker

|            Assistant Research Professor              |
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Received on Fri Mar 23 2012 - 10:30:01 PDT
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