Debugging

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Christoph Mueller edited this page Jul 4, 2018 · 1 revision

[[TOC]]

Debugging

If you are contributing to the code, sometimes errors only show up at runtime. To debug this, you need specific software.

Debugging on Linux

You can either use the command line or a debugger like GDB (ddd with GUI) to compile and debug LPJmL.

Some preconditions:

* tell the system to generate core files. For jobs submitted via lpjsubmit this is automatically set, but for jobs run locally, you want to make sure that ulimit -c is set to unlimited. Either include this line into your .profile

ulimit -cunlimited

or simply execute this command before running the model.

* testing for floating point exceptions, i.e. enable the runtime check for devisions by zero, by including the flag -fpe in the list of arguments, e.g.

lpjml -DFROM_RESTART -fpelpjml.conf

On the command line in your $LPJROOT directory, use

makeclean

to remove any older executable files, then type

makeall

to build new executables. The Makefiles for each sub-directory are already downloaded from the SVN LPJmL trunk. You do not have to write them yourself.

On your local drive, you may also use Eclipse to compile and debug the code. See here how to configure Eclipse.

For debugging, you’ll need to set different compiler sets, so call the configure script with the -debug flag to adjust the Makefile accordingly

configure.sh -debug

or

configure.bat -debug

GDB

call

gdb <YOUREXE> <YOURCOREFILE>

to read the core file. Obviously, this only works if you’re using the executable which was also used to generate the .
With

where

, gdb will trace the origin of the error for you.
Since the update of the cluster in early 2017, gdb may report some error message about missing “additional debug info”. Ciaron and Roger installed a version of gdb that doesn’t have that problem, which you can use by calling

gdb <YOUREXE> <YOURCOREFILE>

.
Make sure you’ve asked to generate core files (see above), if unsure, check ulimit settings with

ulimit -a

Since the update of the cluster in early 2017, gdb cannot handle self-written signal handler, please remove the line source:/trunk/src/tools/enablefpe.c#L55
If LPJmL internal fail commands do not produce proper core files that can be interpreted by gdb, try replacing the abort command source:trunk/src/tools/fail.c with a deliberate segmentation fault. (e.g. define int *ptr=NULL; and assign a value to it instead of calling abort, e.g.

*ptr=0;

Attention: the MPI causes a lot of warning and failure messages wit valgrind. To test your code, it is advisable to not only enable MPI usage on the login nodes via

unsetI_MPI_DAPL_UD_PROVIDER

but to also compile the code without MPI features by removing

 -DUSE_MPI

from the Makefile (Makefile.inc directly or config/Makefile.cluster2015 and then run ./configure.sh -debug again
Then call

makecleanmakeall

valgrind

For valgrind debugging, you need to load the valgrind module

moduleloadvalgrind

and then call

valgrind --leak-check=full --log-file=YOURLOGFILENAMEYOURPROGYOURARGS

which could be e.g.

valgrind --leak-check=full --log-file=val.loglpjml -DFROM_RESTARTlpjml.conf

for more information on valgrind see http://valgrind.org/ and

valgrind --help

Valgrind also detects memory leakages (reading/writing out of array bounds — a very nasty bug to find). It’s a command line tool, so it needs some arguments to do what you want it to do.

Debugging (Windows)

Microsoft Visual Studio Debugger (or Eclipse) allows you to run the program step-by-step and to look into functions sequence and variables content.

  • you can set breakpoints at any line of the source code where you want the debugger to suspend the execution of the program
  • to set a breakpoint on a line of code click in the left margin in the text editor, a red dot should appear
  • then start debugging (F5)
  • the program will run through all steps before the breakpoint line and you will be able to look at its status at that point

Clone this wiki locally

, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
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}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

Skip to content
Debugging
Jump to bottom

Christoph Mueller edited this page Jul 4, 2018
·
1 revision
[[TOC]]
Debugging
If you are contributing to the code, sometimes errors only show up at
runtime. To debug this, you need specific software.
Debugging on Linux
You can either use the command line or a debugger like GDB (ddd with
GUI) to compile and debug LPJmL.
Some preconditions:
* tell the system to generate core files. For jobs submitted via
lpjsubmit this is automatically set, but for jobs run locally,
you want to make sure that ulimit -c is set to
unlimited. Either include this line into your
.profile
ulimit -cunlimited
or simply execute this command before running the model.
* testing for floating point exceptions, i.e. enable the runtime
check for devisions by zero, by including the flag
-fpe in the list of arguments, e.g.
lpjml -DFROM_RESTART -fpelpjml.conf
On the command line in your $LPJROOT directory, use
makeclean
to remove any older executable files, then type
makeall
to build new executables. The Makefiles for each sub-directory are
already downloaded from the SVN LPJmL trunk. You do not have to write
them yourself.
On your local drive, you may also use Eclipse to compile and debug the
code. See here how to configure Eclipse.
For debugging, you’ll need to set different compiler sets, so call the
configure script with the -debug flag to adjust the Makefile accordingly
configure.sh -debug
or
configure.bat -debug
GDB
call
gdb <YOUREXE> <YOURCOREFILE>
to read the core file. Obviously, this only works if you’re using the
executable which was also used to generate the
.

With
where
, gdb will trace the origin of the error for you.

Since the update of the cluster in early 2017, gdb may report some
error message about missing “additional debug info”. Ciaron and Roger
installed a version of gdb that doesn’t have that problem, which you can
use by calling
gdb <YOUREXE> <YOURCOREFILE>
.

Make sure you’ve asked to generate core files (see above), if unsure,
check ulimit settings with
ulimit -a
Since the update of the cluster in early 2017, gdb cannot handle
self-written signal handler, please remove the line
source:/trunk/src/tools/enablefpe.c#L55

If LPJmL internal fail commands do not produce proper core files that
can be interpreted by gdb, try replacing the abort command
source:trunk/src/tools/fail.c with a deliberate segmentation fault.
(e.g. define int *ptr=NULL; and assign a
value to it instead of calling abort, e.g.
*ptr=0;
Attention: the MPI causes a lot of warning and failure messages wit
valgrind. To test your code, it is advisable to not only enable MPI
usage on the login nodes via
unsetI_MPI_DAPL_UD_PROVIDER
but to also compile the code without MPI features by removing
 -DUSE_MPI
from the Makefile (Makefile.inc directly or
config/Makefile.cluster2015 and then run
./configure.sh -debug again

Then call
makecleanmakeall
valgrind
For valgrind debugging, you need to load the valgrind module
moduleloadvalgrind
and then
call
valgrind --leak-check=full --log-file=YOURLOGFILENAMEYOURPROGYOURARGS
which could be
e.g.
valgrind --leak-check=full --log-file=val.loglpjml -DFROM_RESTARTlpjml.conf
for more information on valgrind see http://valgrind.org/ and
valgrind --help
Valgrind also detects memory leakages (reading/writing out of array
bounds — a very nasty bug to find). It’s a command line tool, so it
needs some arguments to do what you want it to do.
Debugging (Windows)
Microsoft Visual Studio
Debugger
(or Eclipse) allows you to run the program step-by-step and to look into
functions sequence and variables content.
  • you can set breakpoints at any line of the source code where you
want the debugger to suspend the execution of the program
  • to set a breakpoint on a line of code click in the left margin in
the text editor, a red dot should appear
  • then start debugging (F5)
  • the program will run through all steps before the breakpoint line
and you will be able to look at its status at that point
Clone this wiki locally

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Debugging
Jump to bottom

Christoph Mueller edited this page Jul 4, 2018
·
1 revision
[[TOC]]
Debugging
If you are contributing to the code, sometimes errors only show up at
runtime. To debug this, you need specific software.
Debugging on Linux
You can either use the command line or a debugger like GDB (ddd with
GUI) to compile and debug LPJmL.
Some preconditions:
* tell the system to generate core files. For jobs submitted via
lpjsubmit this is automatically set, but for jobs run locally,
you want to make sure that ulimit -c is set to
unlimited. Either include this line into your
.profile
ulimit -cunlimited
or simply execute this command before running the model.
* testing for floating point exceptions, i.e. enable the runtime
check for devisions by zero, by including the flag
-fpe in the list of arguments, e.g.
lpjml -DFROM_RESTART -fpelpjml.conf
On the command line in your $LPJROOT directory, use
makeclean
to remove any older executable files, then type
makeall
to build new executables. The Makefiles for each sub-directory are
already downloaded from the SVN LPJmL trunk. You do not have to write
them yourself.
On your local drive, you may also use Eclipse to compile and debug the
code. See here how to configure Eclipse.
For debugging, you’ll need to set different compiler sets, so call the
configure script with the -debug flag to adjust the Makefile accordingly
configure.sh -debug
or
configure.bat -debug
GDB
call
gdb <YOUREXE> <YOURCOREFILE>
to read the core file. Obviously, this only works if you’re using the
executable which was also used to generate the
.

With
where
, gdb will trace the origin of the error for you.

Since the update of the cluster in early 2017, gdb may report some
error message about missing “additional debug info”. Ciaron and Roger
installed a version of gdb that doesn’t have that problem, which you can
use by calling
gdb <YOUREXE> <YOURCOREFILE>
.

Make sure you’ve asked to generate core files (see above), if unsure,
check ulimit settings with
ulimit -a
Since the update of the cluster in early 2017, gdb cannot handle
self-written signal handler, please remove the line
source:/trunk/src/tools/enablefpe.c#L55

If LPJmL internal fail commands do not produce proper core files that
can be interpreted by gdb, try replacing the abort command
source:trunk/src/tools/fail.c with a deliberate segmentation fault.
(e.g. define int *ptr=NULL; and assign a
value to it instead of calling abort, e.g.
*ptr=0;
Attention: the MPI causes a lot of warning and failure messages wit
valgrind. To test your code, it is advisable to not only enable MPI
usage on the login nodes via
unsetI_MPI_DAPL_UD_PROVIDER
but to also compile the code without MPI features by removing
 -DUSE_MPI
from the Makefile (Makefile.inc directly or
config/Makefile.cluster2015 and then run
./configure.sh -debug again

Then call
makecleanmakeall
valgrind
For valgrind debugging, you need to load the valgrind module
moduleloadvalgrind
and then
call
valgrind --leak-check=full --log-file=YOURLOGFILENAMEYOURPROGYOURARGS
which could be
e.g.
valgrind --leak-check=full --log-file=val.loglpjml -DFROM_RESTARTlpjml.conf
for more information on valgrind see http://valgrind.org/ and
valgrind --help
Valgrind also detects memory leakages (reading/writing out of array
bounds — a very nasty bug to find). It’s a command line tool, so it
needs some arguments to do what you want it to do.
Debugging (Windows)
Microsoft Visual Studio
Debugger
(or Eclipse) allows you to run the program step-by-step and to look into
functions sequence and variables content.
  • you can set breakpoints at any line of the source code where you
want the debugger to suspend the execution of the program
  • to set a breakpoint on a line of code click in the left margin in
the text editor, a red dot should appear
  • then start debugging (F5)
  • the program will run through all steps before the breakpoint line
and you will be able to look at its status at that point
Clone this wiki locally

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Debugging
Jump to bottom

Christoph Mueller edited this page Jul 4, 2018
·
1 revision
[[TOC]]
Debugging
If you are contributing to the code, sometimes errors only show up at
runtime. To debug this, you need specific software.
Debugging on Linux
You can either use the command line or a debugger like GDB (ddd with
GUI) to compile and debug LPJmL.
Some preconditions:
* tell the system to generate core files. For jobs submitted via
lpjsubmit this is automatically set, but for jobs run locally,
you want to make sure that ulimit -c is set to
unlimited. Either include this line into your
.profile
ulimit -cunlimited
or simply execute this command before running the model.
* testing for floating point exceptions, i.e. enable the runtime
check for devisions by zero, by including the flag
-fpe in the list of arguments, e.g.
lpjml -DFROM_RESTART -fpelpjml.conf
On the command line in your $LPJROOT directory, use
makeclean
to remove any older executable files, then type
makeall
to build new executables. The Makefiles for each sub-directory are
already downloaded from the SVN LPJmL trunk. You do not have to write
them yourself.
On your local drive, you may also use Eclipse to compile and debug the
code. See here how to configure Eclipse.
For debugging, you’ll need to set different compiler sets, so call the
configure script with the -debug flag to adjust the Makefile accordingly
configure.sh -debug
or
configure.bat -debug
GDB
call
gdb <YOUREXE> <YOURCOREFILE>
to read the core file. Obviously, this only works if you’re using the
executable which was also used to generate the
.

With
where
, gdb will trace the origin of the error for you.

Since the update of the cluster in early 2017, gdb may report some
error message about missing “additional debug info”. Ciaron and Roger
installed a version of gdb that doesn’t have that problem, which you can
use by calling
gdb <YOUREXE> <YOURCOREFILE>
.

Make sure you’ve asked to generate core files (see above), if unsure,
check ulimit settings with
ulimit -a
Since the update of the cluster in early 2017, gdb cannot handle
self-written signal handler, please remove the line
source:/trunk/src/tools/enablefpe.c#L55

If LPJmL internal fail commands do not produce proper core files that
can be interpreted by gdb, try replacing the abort command
source:trunk/src/tools/fail.c with a deliberate segmentation fault.
(e.g. define int *ptr=NULL; and assign a
value to it instead of calling abort, e.g.
*ptr=0;
Attention: the MPI causes a lot of warning and failure messages wit
valgrind. To test your code, it is advisable to not only enable MPI
usage on the login nodes via
unsetI_MPI_DAPL_UD_PROVIDER
but to also compile the code without MPI features by removing
 -DUSE_MPI
from the Makefile (Makefile.inc directly or
config/Makefile.cluster2015 and then run
./configure.sh -debug again

Then call
makecleanmakeall
valgrind
For valgrind debugging, you need to load the valgrind module
moduleloadvalgrind
and then
call
valgrind --leak-check=full --log-file=YOURLOGFILENAMEYOURPROGYOURARGS
which could be
e.g.
valgrind --leak-check=full --log-file=val.loglpjml -DFROM_RESTARTlpjml.conf
for more information on valgrind see http://valgrind.org/ and
valgrind --help
Valgrind also detects memory leakages (reading/writing out of array
bounds — a very nasty bug to find). It’s a command line tool, so it
needs some arguments to do what you want it to do.
Debugging (Windows)
Microsoft Visual Studio
Debugger
(or Eclipse) allows you to run the program step-by-step and to look into
functions sequence and variables content.
  • you can set breakpoints at any line of the source code where you
want the debugger to suspend the execution of the program
  • to set a breakpoint on a line of code click in the left margin in
the text editor, a red dot should appear
  • then start debugging (F5)
  • the program will run through all steps before the breakpoint line
and you will be able to look at its status at that point
Clone this wiki locally

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

Skip to content
Debugging
Jump to bottom

Christoph Mueller edited this page Jul 4, 2018
·
1 revision
[[TOC]]
Debugging
If you are contributing to the code, sometimes errors only show up at
runtime. To debug this, you need specific software.
Debugging on Linux
You can either use the command line or a debugger like GDB (ddd with
GUI) to compile and debug LPJmL.
Some preconditions:
* tell the system to generate core files. For jobs submitted via
lpjsubmit this is automatically set, but for jobs run locally,
you want to make sure that ulimit -c is set to
unlimited. Either include this line into your
.profile
ulimit -cunlimited
or simply execute this command before running the model.
* testing for floating point exceptions, i.e. enable the runtime
check for devisions by zero, by including the flag
-fpe in the list of arguments, e.g.
lpjml -DFROM_RESTART -fpelpjml.conf
On the command line in your $LPJROOT directory, use
makeclean
to remove any older executable files, then type
makeall
to build new executables. The Makefiles for each sub-directory are
already downloaded from the SVN LPJmL trunk. You do not have to write
them yourself.
On your local drive, you may also use Eclipse to compile and debug the
code. See here how to configure Eclipse.
For debugging, you’ll need to set different compiler sets, so call the
configure script with the -debug flag to adjust the Makefile accordingly
configure.sh -debug
or
configure.bat -debug
GDB
call
gdb <YOUREXE> <YOURCOREFILE>
to read the core file. Obviously, this only works if you’re using the
executable which was also used to generate the
.

With
where
, gdb will trace the origin of the error for you.

Since the update of the cluster in early 2017, gdb may report some
error message about missing “additional debug info”. Ciaron and Roger
installed a version of gdb that doesn’t have that problem, which you can
use by calling
gdb <YOUREXE> <YOURCOREFILE>
.

Make sure you’ve asked to generate core files (see above), if unsure,
check ulimit settings with
ulimit -a
Since the update of the cluster in early 2017, gdb cannot handle
self-written signal handler, please remove the line
source:/trunk/src/tools/enablefpe.c#L55

If LPJmL internal fail commands do not produce proper core files that
can be interpreted by gdb, try replacing the abort command
source:trunk/src/tools/fail.c with a deliberate segmentation fault.
(e.g. define int *ptr=NULL; and assign a
value to it instead of calling abort, e.g.
*ptr=0;
Attention: the MPI causes a lot of warning and failure messages wit
valgrind. To test your code, it is advisable to not only enable MPI
usage on the login nodes via
unsetI_MPI_DAPL_UD_PROVIDER
but to also compile the code without MPI features by removing
 -DUSE_MPI
from the Makefile (Makefile.inc directly or
config/Makefile.cluster2015 and then run
./configure.sh -debug again

Then call
makecleanmakeall
valgrind
For valgrind debugging, you need to load the valgrind module
moduleloadvalgrind
and then
call
valgrind --leak-check=full --log-file=YOURLOGFILENAMEYOURPROGYOURARGS
which could be
e.g.
valgrind --leak-check=full --log-file=val.loglpjml -DFROM_RESTARTlpjml.conf
for more information on valgrind see http://valgrind.org/ and
valgrind --help
Valgrind also detects memory leakages (reading/writing out of array
bounds — a very nasty bug to find). It’s a command line tool, so it
needs some arguments to do what you want it to do.
Debugging (Windows)
Microsoft Visual Studio
Debugger
(or Eclipse) allows you to run the program step-by-step and to look into
functions sequence and variables content.
  • you can set breakpoints at any line of the source code where you
want the debugger to suspend the execution of the program
  • to set a breakpoint on a line of code click in the left margin in
the text editor, a red dot should appear
  • then start debugging (F5)
  • the program will run through all steps before the breakpoint line
and you will be able to look at its status at that point
Clone this wiki locally

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Debugging
Jump to bottom

Christoph Mueller edited this page Jul 4, 2018
·
1 revision
[[TOC]]
Debugging
If you are contributing to the code, sometimes errors only show up at
runtime. To debug this, you need specific software.
Debugging on Linux
You can either use the command line or a debugger like GDB (ddd with
GUI) to compile and debug LPJmL.
Some preconditions:
* tell the system to generate core files. For jobs submitted via
lpjsubmit this is automatically set, but for jobs run locally,
you want to make sure that ulimit -c is set to
unlimited. Either include this line into your
.profile
ulimit -cunlimited
or simply execute this command before running the model.
* testing for floating point exceptions, i.e. enable the runtime
check for devisions by zero, by including the flag
-fpe in the list of arguments, e.g.
lpjml -DFROM_RESTART -fpelpjml.conf
On the command line in your $LPJROOT directory, use
makeclean
to remove any older executable files, then type
makeall
to build new executables. The Makefiles for each sub-directory are
already downloaded from the SVN LPJmL trunk. You do not have to write
them yourself.
On your local drive, you may also use Eclipse to compile and debug the
code. See here how to configure Eclipse.
For debugging, you’ll need to set different compiler sets, so call the
configure script with the -debug flag to adjust the Makefile accordingly
configure.sh -debug
or
configure.bat -debug
GDB
call
gdb <YOUREXE> <YOURCOREFILE>
to read the core file. Obviously, this only works if you’re using the
executable which was also used to generate the
.

With
where
, gdb will trace the origin of the error for you.

Since the update of the cluster in early 2017, gdb may report some
error message about missing “additional debug info”. Ciaron and Roger
installed a version of gdb that doesn’t have that problem, which you can
use by calling
gdb <YOUREXE> <YOURCOREFILE>
.

Make sure you’ve asked to generate core files (see above), if unsure,
check ulimit settings with
ulimit -a
Since the update of the cluster in early 2017, gdb cannot handle
self-written signal handler, please remove the line
source:/trunk/src/tools/enablefpe.c#L55

If LPJmL internal fail commands do not produce proper core files that
can be interpreted by gdb, try replacing the abort command
source:trunk/src/tools/fail.c with a deliberate segmentation fault.
(e.g. define int *ptr=NULL; and assign a
value to it instead of calling abort, e.g.
*ptr=0;
Attention: the MPI causes a lot of warning and failure messages wit
valgrind. To test your code, it is advisable to not only enable MPI
usage on the login nodes via
unsetI_MPI_DAPL_UD_PROVIDER
but to also compile the code without MPI features by removing
 -DUSE_MPI
from the Makefile (Makefile.inc directly or
config/Makefile.cluster2015 and then run
./configure.sh -debug again

Then call
makecleanmakeall
valgrind
For valgrind debugging, you need to load the valgrind module
moduleloadvalgrind
and then
call
valgrind --leak-check=full --log-file=YOURLOGFILENAMEYOURPROGYOURARGS
which could be
e.g.
valgrind --leak-check=full --log-file=val.loglpjml -DFROM_RESTARTlpjml.conf
for more information on valgrind see http://valgrind.org/ and
valgrind --help
Valgrind also detects memory leakages (reading/writing out of array
bounds — a very nasty bug to find). It’s a command line tool, so it
needs some arguments to do what you want it to do.
Debugging (Windows)
Microsoft Visual Studio
Debugger
(or Eclipse) allows you to run the program step-by-step and to look into
functions sequence and variables content.
  • you can set breakpoints at any line of the source code where you
want the debugger to suspend the execution of the program
  • to set a breakpoint on a line of code click in the left margin in
the text editor, a red dot should appear
  • then start debugging (F5)
  • the program will run through all steps before the breakpoint line
and you will be able to look at its status at that point
Clone this wiki locally

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Debugging
Jump to bottom

Christoph Mueller edited this page Jul 4, 2018
·
1 revision
[[TOC]]
Debugging
If you are contributing to the code, sometimes errors only show up at
runtime. To debug this, you need specific software.
Debugging on Linux
You can either use the command line or a debugger like GDB (ddd with
GUI) to compile and debug LPJmL.
Some preconditions:
* tell the system to generate core files. For jobs submitted via
lpjsubmit this is automatically set, but for jobs run locally,
you want to make sure that ulimit -c is set to
unlimited. Either include this line into your
.profile
ulimit -cunlimited
or simply execute this command before running the model.
* testing for floating point exceptions, i.e. enable the runtime
check for devisions by zero, by including the flag
-fpe in the list of arguments, e.g.
lpjml -DFROM_RESTART -fpelpjml.conf
On the command line in your $LPJROOT directory, use
makeclean
to remove any older executable files, then type
makeall
to build new executables. The Makefiles for each sub-directory are
already downloaded from the SVN LPJmL trunk. You do not have to write
them yourself.
On your local drive, you may also use Eclipse to compile and debug the
code. See here how to configure Eclipse.
For debugging, you’ll need to set different compiler sets, so call the
configure script with the -debug flag to adjust the Makefile accordingly
configure.sh -debug
or
configure.bat -debug
GDB
call
gdb <YOUREXE> <YOURCOREFILE>
to read the core file. Obviously, this only works if you’re using the
executable which was also used to generate the
.

With
where
, gdb will trace the origin of the error for you.

Since the update of the cluster in early 2017, gdb may report some
error message about missing “additional debug info”. Ciaron and Roger
installed a version of gdb that doesn’t have that problem, which you can
use by calling
gdb <YOUREXE> <YOURCOREFILE>
.

Make sure you’ve asked to generate core files (see above), if unsure,
check ulimit settings with
ulimit -a
Since the update of the cluster in early 2017, gdb cannot handle
self-written signal handler, please remove the line
source:/trunk/src/tools/enablefpe.c#L55

If LPJmL internal fail commands do not produce proper core files that
can be interpreted by gdb, try replacing the abort command
source:trunk/src/tools/fail.c with a deliberate segmentation fault.
(e.g. define int *ptr=NULL; and assign a
value to it instead of calling abort, e.g.
*ptr=0;
Attention: the MPI causes a lot of warning and failure messages wit
valgrind. To test your code, it is advisable to not only enable MPI
usage on the login nodes via
unsetI_MPI_DAPL_UD_PROVIDER
but to also compile the code without MPI features by removing
 -DUSE_MPI
from the Makefile (Makefile.inc directly or
config/Makefile.cluster2015 and then run
./configure.sh -debug again

Then call
makecleanmakeall
valgrind
For valgrind debugging, you need to load the valgrind module
moduleloadvalgrind
and then
call
valgrind --leak-check=full --log-file=YOURLOGFILENAMEYOURPROGYOURARGS
which could be
e.g.
valgrind --leak-check=full --log-file=val.loglpjml -DFROM_RESTARTlpjml.conf
for more information on valgrind see http://valgrind.org/ and
valgrind --help
Valgrind also detects memory leakages (reading/writing out of array
bounds — a very nasty bug to find). It’s a command line tool, so it
needs some arguments to do what you want it to do.
Debugging (Windows)
Microsoft Visual Studio
Debugger
(or Eclipse) allows you to run the program step-by-step and to look into
functions sequence and variables content.
  • you can set breakpoints at any line of the source code where you
want the debugger to suspend the execution of the program
  • to set a breakpoint on a line of code click in the left margin in
the text editor, a red dot should appear
  • then start debugging (F5)
  • the program will run through all steps before the breakpoint line
and you will be able to look at its status at that point
Clone this wiki locally

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

Skip to content
Debugging
Jump to bottom

Christoph Mueller edited this page Jul 4, 2018
·
1 revision
[[TOC]]
Debugging
If you are contributing to the code, sometimes errors only show up at
runtime. To debug this, you need specific software.
Debugging on Linux
You can either use the command line or a debugger like GDB (ddd with
GUI) to compile and debug LPJmL.
Some preconditions:
* tell the system to generate core files. For jobs submitted via
lpjsubmit this is automatically set, but for jobs run locally,
you want to make sure that ulimit -c is set to
unlimited. Either include this line into your
.profile
ulimit -cunlimited
or simply execute this command before running the model.
* testing for floating point exceptions, i.e. enable the runtime
check for devisions by zero, by including the flag
-fpe in the list of arguments, e.g.
lpjml -DFROM_RESTART -fpelpjml.conf
On the command line in your $LPJROOT directory, use
makeclean
to remove any older executable files, then type
makeall
to build new executables. The Makefiles for each sub-directory are
already downloaded from the SVN LPJmL trunk. You do not have to write
them yourself.
On your local drive, you may also use Eclipse to compile and debug the
code. See here how to configure Eclipse.
For debugging, you’ll need to set different compiler sets, so call the
configure script with the -debug flag to adjust the Makefile accordingly
configure.sh -debug
or
configure.bat -debug
GDB
call
gdb <YOUREXE> <YOURCOREFILE>
to read the core file. Obviously, this only works if you’re using the
executable which was also used to generate the
.

With
where
, gdb will trace the origin of the error for you.

Since the update of the cluster in early 2017, gdb may report some
error message about missing “additional debug info”. Ciaron and Roger
installed a version of gdb that doesn’t have that problem, which you can
use by calling
gdb <YOUREXE> <YOURCOREFILE>
.

Make sure you’ve asked to generate core files (see above), if unsure,
check ulimit settings with
ulimit -a
Since the update of the cluster in early 2017, gdb cannot handle
self-written signal handler, please remove the line
source:/trunk/src/tools/enablefpe.c#L55

If LPJmL internal fail commands do not produce proper core files that
can be interpreted by gdb, try replacing the abort command
source:trunk/src/tools/fail.c with a deliberate segmentation fault.
(e.g. define int *ptr=NULL; and assign a
value to it instead of calling abort, e.g.
*ptr=0;
Attention: the MPI causes a lot of warning and failure messages wit
valgrind. To test your code, it is advisable to not only enable MPI
usage on the login nodes via
unsetI_MPI_DAPL_UD_PROVIDER
but to also compile the code without MPI features by removing
 -DUSE_MPI
from the Makefile (Makefile.inc directly or
config/Makefile.cluster2015 and then run
./configure.sh -debug again

Then call
makecleanmakeall
valgrind
For valgrind debugging, you need to load the valgrind module
moduleloadvalgrind
and then
call
valgrind --leak-check=full --log-file=YOURLOGFILENAMEYOURPROGYOURARGS
which could be
e.g.
valgrind --leak-check=full --log-file=val.loglpjml -DFROM_RESTARTlpjml.conf
for more information on valgrind see http://valgrind.org/ and
valgrind --help
Valgrind also detects memory leakages (reading/writing out of array
bounds — a very nasty bug to find). It’s a command line tool, so it
needs some arguments to do what you want it to do.
Debugging (Windows)
Microsoft Visual Studio
Debugger
(or Eclipse) allows you to run the program step-by-step and to look into
functions sequence and variables content.
  • you can set breakpoints at any line of the source code where you
want the debugger to suspend the execution of the program
  • to set a breakpoint on a line of code click in the left margin in
the text editor, a red dot should appear
  • then start debugging (F5)
  • the program will run through all steps before the breakpoint line
and you will be able to look at its status at that point
Clone this wiki locally