timing ​
Implementation level ​
| Type | Status |
|---|---|
| CML extraction template |  |
| HTML5 representation |  |
Template attributes ​
| Attribute | Value |
|---|---|
| source | Amber log |
| id | timing |
| name | Timings |
| pattern | \s*-{20,}.*$\s*5\.\s+TIMINGS.* |
| endPattern | \s*$\s*-{20,}. |
| endPattern2 | ~ |
| endOffset | 1 |
| xml:base | job/timings.xml |
Input ​
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
| NonSetup CPU Time in Major Routines:
|
| Routine Sec %
| ------------------------------
| Nonbond 6798.19 53.24
| Bond 0.00 0.00
| Angle 0.00 0.00
| Dihedral 0.00 0.00
| Shake 431.76 3.38
| RunMD 5257.13 41.17
| Other 282.06 2.21
| ------------------------------
| Total 12769.14
| PME Nonbond Pairlist CPU Time:
|
| Routine Sec %
| ---------------------------------
| Set Up Cit 0.00 0.00
| Build List 0.00 0.00
| ---------------------------------
| Total 0.00 0.00
| PME Direct Force CPU Time:
|
| Routine Sec %
| ---------------------------------
| NonBonded Calc 0.00 0.00
| Exclude Masked 0.00 0.00
| Other 59.60 0.47
| ---------------------------------
| Total 59.60 0.47
| PME Reciprocal Force CPU Time:
|
| Routine Sec %
| ---------------------------------
| 1D bspline 0.00 0.00
| Grid Charges 0.00 0.00
| Scalar Sum 0.00 0.00
| Gradient Sum 0.00 0.00
| FFT 0.00 0.00
| ---------------------------------
| Total 0.00 0.00
| Final Performance Info:
| -----------------------------------------------------
| Average timings for last 100000 steps:
| Elapsed(s) = 25.50 Per Step(ms) = 0.25
| ns/day = 677.69 seconds/ns = 127.49
|
| Average timings for all steps:
| Elapsed(s) = 12766.97 Per Step(ms) = 0.26
| ns/day = 676.75 seconds/ns = 127.67
| -----------------------------------------------------
| Setup CPU time: 0.36 seconds
| NonSetup CPU time: 12769.14 seconds
| Total CPU time: 12769.50 seconds 3.55 hours
| Setup wall time: 0 seconds
| NonSetup wall time: 12767 seconds
| Total wall time: 12767 seconds 3.55 hours
Input ​
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
| Build the list 27.49 (99.73% of List )
| Other 0.08 ( 0.27% of List )
| List time 27.57 (13.07% of Nonbo)
| Short_ene time 156.46 (99.34% of Direc)
| Other 1.03 ( 0.66% of Direc)
| Direct Ewald time 157.49 (85.86% of Ewald)
| Adjust Ewald time 0.70 ( 0.38% of Ewald)
| Self Ewald time 0.01 ( 0.01% of Ewald)
| Fill Bspline coeffs 0.95 ( 3.79% of Recip)
| Fill charge grid 2.35 ( 9.36% of Recip)
| Scalar sum 9.44 (37.67% of Recip)
| Grad sum 4.60 (18.35% of Recip)
| FFT time 7.72 (30.78% of Recip)
| Other 0.01 ( 0.06% of Recip)
| Recip Ewald time 25.07 (13.67% of Ewald)
| Force Adjust 0.02 ( 0.01% of Ewald)
| Virial junk 0.07 ( 0.04% of Ewald)
| Other 0.05 ( 0.03% of Ewald)
| Ewald time 183.42 (86.92% of Nonbo)
| Other 0.02 ( 0.01% of Nonbo)
| Nonbond force 211.01 (99.89% of Force)
| Bond/Angle/Dihedral 0.20 ( 0.10% of Force)
| Other 0.03 ( 0.02% of Force)
| Force time 211.25 (99.39% of Runmd)
| Shake time 0.81 ( 0.38% of Runmd)
| Verlet update time 0.43 ( 0.20% of Runmd)
| Other 0.06 ( 0.03% of Runmd)
| Runmd Time 212.55 (100.0% of Total)
| Other 0.07 ( 0.03% of Total)
| Total time 212.63 (100.0% of ALL )
| Number of list builds : 253
| Highest rstack allocated: 453370
| Highest istack allocated: 7628
| Final Performance Info:
| -----------------------------------------------------
| Average timings for all steps:
| Elapsed(s) = 212.55 Per Step(ms) = 85.02
| ns/day = 2.03 seconds/ns = 42510.43
| -----------------------------------------------------
| Job began at 11:14:57.831 on 11/16/2021
| Setup done at 11:14:57.912 on 11/16/2021
| Run done at 11:18:30.463 on 11/16/2021
| wallclock() was called 110524 times
|3D-RISM memory allocation summary
|Type Maximum Current
|Integer 0.00000 GB 0.00000 GB
|Real 0.00000 GB 0.00000 GB
|Logical 0.00000 GB 0.00000 GB
|Character 0.00000 GB 0.00000 GB
|---------------------------------------
|Total 0.00000 GB 0.00000 GB
Output text ​
xml
<comment class="example.output" id="timing">
<module cmlx:templateRef="timing">
<module cmlx:templateRef="walltime">
<scalar dataType="xsd:double" dictRef="cc:elapsedtime" units="si:s">12766.97</scalar>
<scalar dataType="xsd:double" dictRef="am:elapsedstep" units="nonsi:milliseconds">0.26</scalar>
<scalar dataType="xsd:double" dictRef="am:nsperday">676.75</scalar>
<scalar dataType="xsd:double" dictRef="am:secondsperns">127.67</scalar>
<scalar dataType="xsd:integer" dictRef="cc:wallTime" units="si:s">12767</scalar>
<scalar dataType="xsd:double" dictRef="cc:cpuTime" units="si:s">12769.50</scalar>
</module>
</module>
</comment>Output text ​
xml
<comment class="example.output" id="timing2">
<module cmlx:templateRef="timing">
<module cmlx:templateRef="walltime">
<scalar dataType="xsd:double" dictRef="cc:elapsedtime" units="si:s">212.55</scalar>
<scalar dataType="xsd:double" dictRef="am:elapsedstep" units="nonsi:milliseconds">85.02</scalar>
<scalar dataType="xsd:double" dictRef="am:nsperday">2.03</scalar>
<scalar dataType="xsd:double" dictRef="am:secondsperns">42510.43</scalar>
<scalar dataType="xsd:date" dictRef="cc:runDate">2021-11-16T11:14:57.831</scalar>
<scalar dataType="xsd:date" dictRef="cc:dateEnd">2021-11-16T11:18:30.463</scalar>
</module>
</module>
</comment>Template definition ​
xml
<templateList> <template id="walltime" pattern="\s*\|\s+Final\sPerformance\sInfo:.*" endPattern="\s*" endPattern2=".*[0-9]$\s*\|\s+-{20,}]"> <templateList> <template pattern="\s*\|\s+Average\stimings\sfor\sall\ssteps.*" endPattern="\s*\|\s*" endPattern2="~"> <record /> <record>\s*\|\s+Elapsed\(s\)\s*={F,cc:elapsedtime}Per\sStep\(ms\)\s*={F,am:elapsedstep}</record> <record>\s*\|\s+ns\/day\s*={F,am:nsperday}seconds/ns\s*={F,am:secondsperns}</record> <transform process="pullup" xpath=".//cml:scalar" />
</template>
</templateList>
</template> <template id="cputime" pattern="\s*\|\s+.*Setup\sCPU\stime:.*" endPattern=".*Total\sCPU\stime.*" endOffset="1"> <record repeat="2" /> <record>\s*\|\s+.*Total\sCPU\stime:{F,cc:cpuTime}seconds.*</record>
</template> <template id="walltime2" pattern="\s*\|\s+.*Setup\swall\stime:.*" endPattern="\s+" endPattern2="~" endOffset="1"> <record repeat="2" /> <record>\s*\|\s+.*Total\swall\stime:{I,cc:wallTime}seconds.*</record>
</template> <template id="jobDates" pattern="\s*\|\s*Job\s*began\s*at.*" endPattern="\s*\|\s*Run\s*done\s*at.*" endOffset="1"> <record>\s*\|\s*Job\s*began\s*at{X,cc:runDate}</record> <record /> <record>\s*\|\s*Run\s*done\s*at{X,cc:dateEnd}</record> <transform process="createDate" xpath=".//cml:scalar[@dictRef='cc:runDate']" format="HH:mm:ss.SSS 'on' MM/dd/yyyy" /> <transform process="createDate" xpath=".//cml:scalar[@dictRef='cc:dateEnd']" format="HH:mm:ss.SSS 'on' MM/dd/yyyy" />
</template>
</templateList>
<transform process="addUnits" xpath=".//cml:scalar[@dictRef='cc:elapsedtime']" value="si:s" />
<transform process="addUnits" xpath=".//cml:scalar[@dictRef='am:elapsedstep']" value="nonsi:milliseconds" />
<transform process="addUnits" xpath=".//cml:scalar[@dictRef='cc:wallTime']" value="si:s" />
<transform process="addUnits" xpath=".//cml:scalar[@dictRef='cc:cpuTime']" value="si:s" />
<transform process="pullup" xpath=".//cml:module[@cmlx:templateRef='walltime']//cml:scalar" repeat="2" />
<transform process="moveRelative" xpath=".//cml:module[@cmlx:templateRef='walltime2']//cml:scalar" to="ancestor::cml:module[@cmlx:templateRef='timing']//cml:module[@cmlx:templateRef='walltime']" />
<transform process="moveRelative" xpath=".//cml:module[@cmlx:templateRef='cputime']//cml:scalar" to="ancestor::cml:module[@cmlx:templateRef='timing']//cml:module[@cmlx:templateRef='walltime']" />
<transform process="moveRelative" xpath=".//cml:module[@cmlx:templateRef='jobDates']//cml:scalar" to="ancestor::cml:module[@cmlx:templateRef='timing']//cml:module[@cmlx:templateRef='walltime']" />
<transform process="delete" xpath=".//cml:list" />
<transform process="delete" xpath=".//cml:module[@cmlx:templateRef='walltime2']" />
<transform process="delete" xpath=".//cml:module[@cmlx:templateRef='cputime']" />
<transform process="delete" xpath=".//cml:module[@cmlx:templateRef='jobDates']" />
<transform process="delete" xpath=".//cml:module[count(*) = 0]" />