Hi Scott,
Thanks for your reply! The instructions are those provided by the PSC, but they only differ from the Amber manual in that they indicate what modules to load and to disable mdgx. I checked the log files, and I see one test that failed:
FAILURE: check nve.out.dif
/jet/home/mag14011/amber22/test/pgm_512wat
189c189
< Etot = 0.0156 EKtot = 3.2681 EPtot = 3.2825
> Etot = 0.0183 EKtot = 3.2681 EPtot = 3.2824
### Maximum absolute error in matching lines = 2.70e-03 at line 189 field 3
### Maximum relative error in matching lines = 1.73e-01 at line 189 field 3
The possible failure seem to be simply round-off issues.
possible FAILURE: check bis_2.out.dif
/jet/home/mag14011/amber22/AmberTools/test/py_resp/bis-naphthyl/resp-ind
238c238
< qchnge = 2.6466137125E-11
> qchnge = 2.6466053481E-11
### Maximum absolute error in matching lines = 8.36e-17 at line 238 field 3
### Maximum relative error in matching lines = 3.16e-06 at line 238 field 3
---------------------------------------
possible FAILURE: check spc.xvv.other.dif
/jet/home/mag14011/amber22/AmberTools/test/rism1d/spc-kh
43c43
< 5.9583872041744979E-1 -8.8128430347391506E-1
> 5.9583872875081068E-1 -8.8128602837469283E-1
### Maximum absolute error in matching lines = 1.72e-06 at line 43 field 2
### Maximum relative error in matching lines = 1.96e-06 at line 43 field 2
I’m not sure what to make of the failure. Should I be concerned? What should I try?
Best,
Matthew
> On Nov 10, 2022, at 2:07 AM, Scott Brozell <sbrozell.comcast.net> wrote:
>
> *Message sent from a system outside of UConn.*
>
>
> Hi,
>
> On Wed, Nov 09, 2022 at 09:55:25AM -0600, Matthew Guberman-Pfeffer via AMBER wrote:
>> I am trying to install AMBER, first the serial version, and ultimately the GPU-enalbed version.
>>
>> I???m trying to do the installation on my account at the PSC (I was told each user has to install it for his/herself), but I???m having trouble. Below is the issue:
>>
>> The provided instructions say "mdgx was giving an error message and it is no longer used, so, in
>> the run.cmake add -DDISABLE_TOOLS=???mdgx???
>>
>> I found run_cmake, not run.cmake. Assuming it???s the same file, I added -DDISABLE_TOOLS=???mdgx???, but cmake complained:
>>
>> Parse error in command line argument: -DDISABLE_TOOLS
>> Should be: VAR:type=value
>> CMake Error: No cmake script provided.
>> CMake Error: Problem processing arguments. Aborting.
>>
>> If I omit -DDISABLE_TOOLS, cmake works, and the following installation looks fine, but when I run the tests, I get the below errors:
>>
>> possible FAILURE: check bis_2.out.dif
>> possible FAILURE: check spc.xvv.other.dif
>> possible FAILURE: (ignored) check /jet/home/mag14011/amber22/AmberTools/src/FEW/examples/test/calc_a_1t/AMT/pqr_snaps/AMT_rec.pqr.3.dif
>> possible FAILURE: check nve.out.dif
>> possible FAILURE: (ignored) check min.out.dif
>>
>> These tests don???t appear to have anything to do with mdgx unless I???m mistaken. How can I resolve these (possible) failures? I don???t know what they mean.
>
>
> What is the reference for the instructions you are following ?
> Presumably these are not the ones in the Amber manual.
> run_cmake is indeed the Amber documented place to start;
> see ambermd.org/Manuals.php
>
> Your cmake problem is due to the use of quotes since this worked for me:
> -DDISABLE_TOOLS=mdgx
> .
> .
> .
> -- NOT Building Tools:
> ...
> -- mdgx - Disabled by user
> -- **************************************************************************
>
>
> To check the possible failures, see the files under amber22/logs
> The installation section of our manual also has advice on checking
> the tests.
>
> scott
>
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Received on Thu Nov 10 2022 - 05:30:02 PST
