AMBER Archive (2008)

Subject: Re: AMBER: Amber9 Installation Problem

From: trudy_at_uoguelph.ca
Date: Thu Mar 20 2008 - 17:51:08 CDT

Thanks very much for the suggestions. As it turns out the system was
not configured to use the LD_LIBRARY_PATH by default (new
system) and I hadn't double checked that before compiling. So, that's
fixed now. Ifort version 10 still does not work for the same
incompatibility reasons as before, but the 9.1.x's now work. With the
ifort installation, the tests run successfully now without the several
major failures that I mentioned previously for g95. The ptraj test
runs without any problems. I haven't yet retried with g95, but the
errors with my last attempt were of this magnitude:

TEST_FAILURES.diff file from previous g95 installation:

possible FAILURE: check cytosine.out.dif
/usr/local/Amber/amber9/test/cytosine
99,100c99,100
< NSTEP = 2 TIME(PS) = 5420.004 TEMP(K) = 300.46
PRESS = -32.0
< Etot = -608.0823 EKtot = 1060.4055 EPtot =
-1668.4878 

---
NSTEP =        2   TIME(PS) =    5420.004  TEMP(K) =   300.49  PRESS =    33.2
Etot   =      -664.1291  EKtot   =      1060.4894  EPtot      =     -1724.6185

Notice the large differences between the Etot values.

Other errors:

possible FAILURE:  check les.gb1.diffcrd.out.dif
/usr/local/Amber/amber9/test/LES_GB
89c89
<  Etot   =        36.2961  EKtot   =        49.8695  EPtot      =      
   -13.5734
---
>  Etot   =        35.3923  EKtot   =        49.8693  EPtot      =      
>   -14.4771
--------
---------
--------

possible FAILURE:  check les.gb1.samecrd.out.dif
/usr/local/Amber/amber9/test/LES_GB
84,85c84,85
<  NSTEP =        2   TIME(PS) = 1000010.002  TEMP(K) =     7.93   
PRESS =     0.
<  Etot   =       -27.5622  EKtot   =         0.8587  EPtot      =      
   -28.4209
---
>  NSTEP =        2   TIME(PS) = 1000010.002  TEMP(K) =     7.90   
> PRESS =     0.
>  Etot   =       -28.6584  EKtot   =         0.8551  EPtot      =      
>   -29.5136
--------
---------
--------

possible FAILURE:  check les.gb5.samecrd.out.dif
/usr/local/Amber/amber9/test/LES_GB
84,85c84,85
<  NSTEP =        2   TIME(PS) = 1000010.002  TEMP(K) =     7.95   
PRESS =     0.
<  Etot   =       -28.1445  EKtot   =         0.8611  EPtot      =      
   -29.0056
---
>  NSTEP =        2   TIME(PS) = 1000010.002  TEMP(K) =     7.91   
> PRESS =     0.
>  Etot   =       -29.3327  EKtot   =         0.8562  EPtot      =      
>   -30.1889
--------
---------
--------
possible FAILURE:  check les.gb7.samecrd.out.dif
/usr/local/Amber/amber9/test/LES_GB
85,86c85,86
<  NSTEP =        2   TIME(PS) = 1000010.002  TEMP(K) =     7.91   
PRESS =     0.
<  Etot   =       -27.4582  EKtot   =         0.8568  EPtot      =      
   -28.3150
---
>  NSTEP =        2   TIME(PS) = 1000010.002  TEMP(K) =     7.89   
> PRESS =     0.
>  Etot   =       -27.9747  EKtot   =         0.8549  EPtot      =      
>   -28.8296
--------
---------
--------

and so forth,

With the current apparently successful installation using ifort, most  
of the errors are
the insignificant ones at the fourth decimal place. For example EGB:

possible FAILURE:  check mdout.jar.dif
/usr/local/Amber/amber9/test/jar
180c180
<  EELEC  =        79.1435  EGB     =     -2602.0110  RESTRAINT  =      
     0.0815
---
EELEC  =        79.1435  EGB     =     -2602.0109  RESTRAINT  =         0.0815
---------------------------------------

The only exception is this one:

possible FAILURE:  check amoeba_jac.mdout.dif
/usr/local/Amber/amber9/test/amoeba_jac
206c206
<  EKCMT  =         0.  VIRIAL  =         0.  VOLUME     =         0.0013
---
EKCMT  =         0.  VIRIAL  =         0.  VOLUME     =         0.0028

Do you think that the differences in volume here is significant?

Quoting "David A. Case" <case_at_scripps.edu>:

> On Wed, Mar 19, 2008, trudy_at_uoguelph.ca wrote:
>>
>> I am currently trying to install Amber 9 on a 64 bit Xeon machine with
>> RHEL 5.1 as the operating system. I used gcc [version: gcc (GCC) 4.1.2
>> 20070626 (Red Hat 4.1.2-14) ]  and g95  [version: G95 (GCC 4.0.3 (g95
>> 0.90!) Jul 27 2006)] (./configure g95) and the compilation was
>> succesful, and I did not notice any errors along the way. But, when I
>> ran the test suite, several of the tests gave results that were
>> significantly far from what was expected, and in particular the ptraj
>> module completely crashed with the following errors:
>> ----------------------------------------
>> # make test.ptraj
>> cd ptraj_matrix; ./Run.matrix
>>
>> ptraj: analyze fluctuation matrices
>> Segmentation fault
>>   ./Run.matrix:  Program error
>
> Are you sure you are planning to analyze fluctuation matrices in   
> ptraj?  (This
> is a very specialized calculation.)
>
> If not, you should probably just move on to something else...a newly  
>  rewritten
> ptraj (all in C) will be released in a few weeks.  So, people are not likely
> to be highly motivated to try to track down your bug.
>
> As to the "other tests" that failed, we would need to see details.  I note
> that your g95 is 20 months old: it *might* be worth downloading a   
> newer version
> from www.g95.org.  But it might also be that your installation is (almost)
> fully functional as is.
>
>> ifort -c -w95   -mp1 -O0   -o new2oldparm.o _new2oldparm.f
>> ifort: error #10149: option '-cxxlib-gcc' not supported with the
>> current installed GCC
>
> This has nothing to do with Amber code: errors in new2oldparm.f are   
> invariably
> problems with the compiler installation.  Make sure that you can compile
> simple fortran programs on your machine.
>
> Others on the list may know the answer to how to install ifort on Xeons.
> Did you Google on the error message listed above?
>
> ...dac
>
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