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>PsN
:: Directory Structure
</title
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129 style
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130 <div
class="style1" align
="right">Directory Structure
</div
>
133 style
="position: absolute; left: 226px; top: 188px; width: 497px; height: 431px; z-index: 2; visibility: visible;">
134 <p align
="justify">Here follows an example directory listing
. This particular run is from an
<strong
>scm
</strong
> with five parameter covariate relations
. The files
and directories are listed in roughly the order they were created
. The blue
and green boxes provide an explanatory text
for the directory content
. </p
>
135 <p align
="justify"> The names
, order
or existance of files
and directories are not set in stone
, but they should give you an idea of what a PsN tool run can produce
. Click on the highlighted direcories
and files to display a summary of their
function. </p
>
136 <table width
="100%" border
="0" cellspacing
="0" cellpadding
="0">
138 <td colspan
="4"><tt
><img src
="gfx/folder.open.gif" width
="27" height
="22" hspace
="5" align
="absbottom">scm_dir1
</tt
></td
>
141 <td width
="4%"><tt
></tt
></td
>
142 <td colspan
="3"><tt onClick
="MM_showHideLayers('origmodelfitdir','','show','nmrun','','hide')"><img src
="gfx/folder.open.gif" width
="27" height
="22" hspace
="5" align
="absbottom"><a name
="origmodelfitdir"></a
><a href
="#origmodelfitdir" onClick
="MM_showHideLayers('origmodelfitdir','','show','nmrun','','hide','m11','','hide','m12','','hide','modelfit','','hide','logs','','hide','scm','','hide')">orig_modelfit_dir1
</a
></tt
></td
>
146 <td width
="4%"><tt
></tt
></td
>
147 <td colspan
="2"><tt onClick
="MM_showHideLayers('origmodelfitdir','','hide','nmrun','','show')"><img src
="gfx/folder.open.gif" width
="27" height
="22" hspace
="5" align
="absbottom"><a name
="nmrun"></a
><a href
="#nmrun" onClick
="MM_showHideLayers('origmodelfitdir','','hide','nmrun','','show','m11','','hide','m12','','hide','modelfit','','hide','logs','','hide','scm','','hide')">NM_run1
</a
></tt
></td
>
152 <td width
="4%"> 
;</td
>
154 <dt
><code
><img src
="gfx/file.gif" width
="20" height
="21" hspace
="5" vspace
="2" align
="absbottom">FCON
</code
></dt
>
155 <dt
><code
><img src
="gfx/file.gif" width
="20" height
="21" hspace
="5" vspace
="2" align
="absbottom">FCON
.0</code
></dt
>
156 <dt
><code
><img src
="gfx/file.gif" width
="20" height
="21" hspace
="5" vspace
="2" align
="absbottom">FCON
.1</code
></dt
>
157 <dt
><code
><img src
="gfx/file.gif" width
="20" height
="21" hspace
="5" vspace
="2" align
="absbottom">FCON
.orig
</code
></dt
>
158 <dt
><code
><img src
="gfx/file.gif" width
="20" height
="21" hspace
="5" vspace
="2" align
="absbottom">FDATA
</code
></dt
>
159 <dt
><code
><img src
="gfx/file.gif" width
="20" height
="21" hspace
="5" vspace
="2" align
="absbottom">FREPORT
</code
></dt
>
160 <dt
><code
><img src
="gfx/file.gif" width
="20" height
="21" hspace
="5" vspace
="2" align
="absbottom">FSTREAM
</code
></dt
>
161 <dt
><code
><img src
="gfx/file.gif" width
="20" height
="21" hspace
="5" vspace
="2" align
="absbottom">FSUBS
</code
></dt
>
162 <dt
><code
><img src
="gfx/file.gif" width
="20" height
="21" hspace
="5" vspace
="2" align
="absbottom">FSUBS
.f
</code
></dt
>
163 <dt
><code
><img src
="gfx/file.gif" width
="20" height
="21" hspace
="5" vspace
="2" align
="absbottom">LINK
.LNK
</code
></dt
>
164 <dt
><code
><img src
="gfx/file.gif" width
="20" height
="21" hspace
="5" vspace
="2" align
="absbottom">PRDERR
</code
></dt
>
165 <dt
><code
><img src
="gfx/file.gif" width
="20" height
="21" hspace
="5" vspace
="2" align
="absbottom">compilation_output
.txt
</code
></dt
>
166 <dt
><code
><img src
="gfx/file.gif" width
="20" height
="21" hspace
="5" vspace
="2" align
="absbottom">data6_multi
.dta
</code
></dt
>
167 <dt
><code
><img src
="gfx/file.gif" width
="20" height
="21" hspace
="5" vspace
="2" align
="absbottom">data6_single
.dta
</code
></dt
>
168 <dt
><code
><img src
="gfx/file.gif" width
="20" height
="21" hspace
="5" vspace
="2" align
="absbottom">done
</code
></dt
>
169 <dt
><code
><img src
="gfx/file.gif" width
="20" height
="21" hspace
="5" vspace
="2" align
="absbottom">get_sub0
.f
</code
></dt
>
170 <dt
><code
><img src
="gfx/file.gif" width
="20" height
="21" hspace
="5" vspace
="2" align
="absbottom">msf5
</code
></dt
>
171 <dt
><code
><img src
="gfx/file.gif" width
="20" height
="21" hspace
="5" vspace
="2" align
="absbottom">psn
.lst
</code
></dt
>
172 <dt
><code
><img src
="gfx/file.gif" width
="20" height
="21" hspace
="5" vspace
="2" align
="absbottom">psn
.lst
.0</code
></dt
>
173 <dt
><code
><img src
="gfx/file.gif" width
="20" height
="21" hspace
="5" vspace
="2" align
="absbottom">psn
.lst
.1</code
></dt
>
174 <dt
><code
><img src
="gfx/file.gif" width
="20" height
="21" hspace
="5" vspace
="2" align
="absbottom">psn
.mod
</code
></dt
>
175 <dt
><code
><img src
="gfx/file.gif" width
="20" height
="21" hspace
="5" vspace
="2" align
="absbottom">reader0
.f
</code
></dt
>
181 <td colspan
="2"><tt
><img src
="gfx/folder.open.gif" width
="27" height
="22" hspace
="5" align
="absbottom"><a name
="m11"></a
><a href
="#m11" onClick
="MM_showHideLayers('origmodelfitdir','','hide','nmrun','','hide','m11','','show','m12','','hide','modelfit','','hide','logs','','hide','scm','','hide')">m1
</a
></tt
></td
>
187 <td
><code
><img src
="gfx/file.gif" width
="20" height
="21" hspace
="5" vspace
="2" align
="absbottom">prepared_models
.log
</code
></td
>
193 <dt
><code
><img src
="gfx/file.gif" width
="20" height
="21" hspace
="5" vspace
="2" align
="absbottom">model_NMrun_translation
.txt
</code
></dt
>
194 <dt
><code
><img src
="gfx/file.gif" width
="20" height
="21" hspace
="5" vspace
="2" align
="absbottom">modelfit
.log
</code
></dt
>
195 <dt
><code
><img src
="gfx/file.gif" width
="20" height
="21" hspace
="5" vspace
="2" align
="absbottom">resume
.file
</code
></dt
>
200 <td colspan
="3"><tt onClick
="MM_showHideLayers('origmodelfitdir','','hide','nmrun','','hide','m11','','hide','m12','','show')"><img src
="gfx/folder.open.gif" width
="27" height
="22" hspace
="5" align
="absbottom"><a name
="m12"></a
><a href
="#m12" onClick
="MM_showHideLayers('origmodelfitdir','','hide','nmrun','','hide','m11','','hide','m12','','show','modelfit','','hide','logs','','hide','scm','','hide')">m1
</a
></tt
></td
>
206 <dt
><code
><img src
="gfx/file.gif" width
="20" height
="21" hspace
="5" vspace
="2" align
="absbottom">BAAGE2
.mod
</code
></dt
>
207 <dt
><code
><img src
="gfx/file.gif" width
="20" height
="21" hspace
="5" vspace
="2" align
="absbottom">BAALKO2
.mod
</code
></dt
>
208 <dt
><code
><img src
="gfx/file.gif" width
="20" height
="21" hspace
="5" vspace
="2" align
="absbottom">BASEX2
.mod
</code
></dt
>
209 <dt
><code
><img src
="gfx/file.gif" width
="20" height
="21" hspace
="5" vspace
="2" align
="absbottom">BASMOK2
.mod
</code
></dt
>
210 <dt
><code
><img src
="gfx/file.gif" width
="20" height
="21" hspace
="5" vspace
="1" align
="absbottom">BAWT2
.mod
</code
></dt
>
211 <dt
><code
><img src
="gfx/file.gif" width
="20" height
="21" hspace
="5" vspace
="2" align
="absbottom">BAAGE2
.lst
</code
></dt
>
212 <dt
><code
><img src
="gfx/file.gif" width
="20" height
="21" hspace
="5" vspace
="2" align
="absbottom">BAALKO2
.lst
</code
></dt
>
213 <dt
><code
><img src
="gfx/file.gif" width
="20" height
="21" hspace
="5" vspace
="2" align
="absbottom">BASEX2
.lst
</code
></dt
>
214 <dt
><code
><img src
="gfx/file.gif" width
="20" height
="21" hspace
="5" vspace
="2" align
="absbottom">BASMOK2
.lst
</code
></dt
>
215 <dt
><code
><img src
="gfx/file.gif" width
="20" height
="21" hspace
="5" vspace
="2" align
="absbottom">BAWT2
.lst
</code
></dt
>
216 <dt
><code
><img src
="gfx/file.gif" width
="20" height
="21" hspace
="5" vspace
="2" align
="absbottom">done
</code
></dt
>
217 <dt
><code
><img src
="gfx/file.gif" width
="20" height
="21" hspace
="5" vspace
="2" align
="absbottom">done
.log
</code
></dt
>
218 <dt
><code
><img src
="gfx/file.gif" width
="20" height
="21" hspace
="5" vspace
="2" align
="absbottom">prepared_models
.log
</code
></dt
>
223 <td colspan
="3"><tt
><img src
="gfx/folder.open.gif" width
="27" height
="22" hspace
="5" align
="absbottom"><a name
="modelfit"></a
><a href
="#modelfit" onClick
="MM_showHideLayers('origmodelfitdir','','hide','nmrun','','hide','m11','','hide','m12','','hide','modelfit','','show','logs','','hide','scm','','hide')">modelfit_dir1
</a
></tt
></td
>
228 <td colspan
="2"><p
><tt
><img src
="gfx/folder.gif" width
="20" height
="22" hspace
="5" align
="absbottom">NM_run1
<br
>
229 <img src
="gfx/folder.gif" width
="20" height
="22" hspace
="5" align
="absbottom">NM_run2
<br
>
230 <img src
="gfx/folder.gif" width
="20" height
="22" hspace
="5" align
="absbottom">NM_run3
<br
>
231 <img src
="gfx/folder.gif" width
="20" height
="22" hspace
="5" align
="absbottom">NM_run4
<br
>
232 <img src
="gfx/folder.gif" width
="20" height
="22" hspace
="5" align
="absbottom">NM_run5
<br
>
233 <img src
="gfx/folder.gif" width
="20" height
="22" hspace
="5" align
="absbottom">m1
<br
>
234 <img src
="gfx/folder.gif" width
="20" height
="22" hspace
="5" align
="absbottom">m2
<br
>
235 <img src
="gfx/folder.gif" width
="20" height
="22" hspace
="5" align
="absbottom">m3
<br
>
236 <img src
="gfx/folder.gif" width
="20" height
="22" hspace
="5" align
="absbottom">m4
<br
>
237 <img src
="gfx/folder.gif" width
="20" height
="22" hspace
="5" align
="absbottom">m5
<br
>
238 </tt
><code
><img src
="gfx/file.gif" width
="20" height
="21" hspace
="5" vspace
="2" align
="absbottom">model_NMrun_translation
.txt
<br
>
239 </code
><code
><img src
="gfx/file.gif" width
="20" height
="21" hspace
="5" vspace
="2" align
="absbottom">resume
.file
</code
></p
></td
>
243 <td colspan
="3"><tt
><img src
="gfx/folder.open.gif" width
="27" height
="22" hspace
="5" align
="absbottom"><a name
="scm"></a
><a href
="#scm" onClick
="MM_showHideLayers('origmodelfitdir','','hide','nmrun','','hide','m11','','hide','m12','','hide','modelfit','','hide','logs','','hide','scm','','show')">scm_dir1
</a
></tt
></td
>
248 <td colspan
="2"><tt
><img src
="gfx/folder.gif" width
="20" height
="22" hspace
="5" align
="absbottom">m1
<br
>
249 <img src
="gfx/folder.gif" width
="20" height
="22" hspace
="5" align
="absbottom">modelfit_dir1
<br
>
250 <code
><img src
="gfx/file.gif" width
="20" height
="21" hspace
="5" vspace
="2" align
="absbottom">modelfit1
.log
</code
></tt
></td
>
255 <dt
><code
><img src
="gfx/file.gif" width
="20" height
="21" hspace
="5" vspace
="2" align
="absbottom"><a name
="logs"></a
><a href
="#logs" onClick
="MM_showHideLayers('origmodelfitdir','','hide','nmrun','','hide','m11','','hide','m12','','hide','modelfit','','hide','logs','','show','scm','','hide')">modelfit1
.log
</a
></code
></dt
>
256 <dt
><code
><img src
="gfx/file.gif" width
="20" height
="21" hspace
="5" vspace
="2" align
="absbottom"><a href
="#logs" onClick
="MM_showHideLayers('origmodelfitdir','','hide','nmrun','','hide','m11','','hide','m12','','hide','modelfit','','hide','logs','','show','scm','','hide')">psn_results
.csv
</a
></code
></dt
>
257 <dt
><code
><img src
="gfx/file.gif" width
="20" height
="21" hspace
="5" vspace
="2" align
="absbottom"><a href
="#logs" onClick
="MM_showHideLayers('origmodelfitdir','','hide','nmrun','','hide','m11','','hide','m12','','hide','modelfit','','hide','logs','','show','scm','','hide')">scmlog_parallel1
.txt
</a
></code
></dt
>
258 <dd
><code
></code
></dd
>
263 <div id
="origmodelfitdir" style
="position:absolute; left:495px; top:328px; width:261px; height:152px; z-index:3; visibility: hidden;">
264 <div align
="left">This is the
<code
>orig_modelfit_dir1
</code
> which is created
for any input model which is not run prior to the PsN tool
. The most important files in this directory is
<tt
>model_NMrun_translation
.txt
</tt
> which lists the names of the original model file names
and in which
<tt
>NM_run
</tt
> directory they have been run
. The
<tt
>modelfit
.log
</tt
> which lists a brief summary
for each NONMEM run
, and whether it was successful
or not
. </div
>
266 <div id
="nmrun" style
="position:absolute; left:495px; top:328px; width:261px; height:309px; z-index:3; visibility: hidden;">
267 <p align
="left">This is a typical NONMEM run directory
. This is the ordinary output from NONMEM with a few additions
. The model that is run is in
<tt
>psn
.mod
</tt
> and the corresponding output is in
<tt
>psn
.lst
</tt
>. In this particular run the data set was to wide
for NONMEM so it has been split into two
<tt
>data6_multi
.dta
</tt
> and <tt
>data6_single
.dta
</tt
>. To make NONMEM cope with the extra data there is extra fortran code in
<tt
>reader0
.f
</tt
> and <tt
>get_sub0
.f
</tt
>, there may be more files like this
, they will be named
<tt
>reader1
.f
</tt
>, <tt
>reader2
.f
</tt
> and so forth
.</p
>
268 <p align
="left">Special
for this run is the
<tt
>FCON
.0</tt
>,<tt
> FCON
.1</tt
>,<tt
> psn
.lst
.0</tt
> and <tt
>psn
.lst
.1</tt
>. They come from the reruns that PsN does when NONMEM fails
. In the
<tt
>FCON
</tt
> files are
new intial estimates
and in
<tt
>psn
.lst
</tt
> is the result
for each rerun
. <tt
>FCON
.orig
</tt
> is the original file that
<tt
>nmtran
</tt
> created
and <tt
>FCON
</tt
> corresponds to the last run
. </p
>
270 <div id
="m11" style
="position:absolute; left:495px; top:921px; width:261px; height:152px; z-index:3; visibility: hidden;">
271 <div align
="left">The
<tt
>m1
</tt
> directory is not very interesting
for modelfit directories
. Look at the
<tt
>m1
</tt
> directory
for the
<b
>scm
</b
> further down
. </div
>
273 <div id
="m12" style
="position:absolute; left:495px; top:1037px; width:261px; height:152px; z-index:3; visibility: hidden;">
274 <div align
="left">In the
<b
>scm
</b
> the
<tt
>m1
</tt
> directories contain what we call prepared models
. Before the
<b
>scm
</b
> step is run we creat all modelfiles that will be evaluated in this directory
. When the execution is finished we place the ouput files here
, also ther is the
<tt
>done
</tt
> file which is created when the
<b
>scm
</b
> step is
finished (It is used by PsN in resume mode
, to figure out
if this step needs to be redone
). <tt
>done
.log
</tt
> and <tt
>prepared_models
.log
</tt
> is
for internal PsN
use only
. You should not rely on them
for information
. </div
>
276 <div id
="modelfit" style
="position:absolute; left:495px; top:1388px; width:261px; height:152px; z-index:3; visibility: hidden;">
277 <div align
="left">This is the modelfit directory
for the
<b
>scm
</b
>, in here you may find all of the models
for this
<b
>scm
</b
> step that have been completed
. It follows the same structure
as <tt
>orig_modelfit_dir1
</tt
> above
. The files listed in
<tt
>model_NMrun_translation
.txt
</tt
> refers to files in the
<tt
>m1
</tt
> directory
. </div
>
279 <div id
="logs" style
="position:absolute; left:495px; top:1772px; width:261px; height:44px; z-index:3; visibility: hidden;">
280 <div align
="left">These are the log files
for the outermost tool
, the
<b
>scm
</b
> in this
case. </div
>
282 <div id
="scm" style
="position:absolute; left:495px; top:1681px; width:261px; height:152px; z-index:3; visibility: hidden;">
283 <div align
="left">This
<b
>scm
</b
> directory contains the files created by the second
<b
>scm
</b
> step
. It follows the same structure
as the current
<b
>scm
</b
> directory
. When the
<b
>scm
</b
> finishes no further
<b
>scm
</b
> directories are created
. Possibly there is a
<tt
>scm_dir2
</tt
> in the top level
<b
>scm
</b
> , then in
<tt
>scm_dir2
</tt
> is the files created
for the backwards step
. </div
>
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