Coding tips DOCK 3.7: Difference between revisions
Nir London (talk | contribs) |
Nir London (talk | contribs) |
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<code> | <code> | ||
pgdbg> break run_search !set a break point at the beginning of the function run_search | pgdbg> break run_search !set a break point at the beginning of the function run_search <br> | ||
pgdbg> run ! runs until hits break point | pgdbg> run ! runs until hits break point <br> | ||
pgdbg> s ! steps through the different functions (use n to skip over function calls) | pgdbg> s ! steps through the different functions (use n to skip over function calls) <br> | ||
pgdbg> c ! continues the run until hits the next break point | pgdbg> c ! continues the run until hits the next break point <br> | ||
</code> | </code> | ||
Latest revision as of 16:44, 3 April 2014
Adding an INDOCK parameter:
To add an option to the INDOCK file that will be parsed and read into DOCK edit the following files:
Add a declaration of the variable that will contain your parameter to optionstype.f
logical :: dockovalent
Set the default value for your variable in setdef.f
options0%dockovalent = .false.
Parse input value (or keyword value) from INDOCK in dokw.f
else if (keywrd .eq. 'dockovalent') then
call tolow(args)
if (nf .lt. 1) then
options0%dockovalent = .false. !off by default
else if (args(1:1) .eq. 'y') then
options0%dockovalent = .true.
else
options0%dockovalent = .false.
endif
Debugging with pgf
On sgehead (or anywhere you have access to the pgf tools), from your run dir, type:
pgdbg .../dock64 where the parameter is the binary result of your compilation
while in the debugger, you can type 'help' to get all available commands.
you can type 'help command' (e.g. 'help break') to get specific usage for that function.
Below are a couple of useful scenarios:
pgdbg> run !run the binary
!-- program segfaults but you don't know where --!
pgdbg> stacktrace ! gives you the call stack to identify the crash site
pgdbg> break run_search !set a break point at the beginning of the function run_search
pgdbg> run ! runs until hits break point
pgdbg> s ! steps through the different functions (use n to skip over function calls)
pgdbg> c ! continues the run until hits the next break point