swmmout
swmmtoolbox catalog sydney_sps.out
get all the variables in the outfile
swmmtoolbox extract sydney_sps.out link,link597,1 >> link597.txt
swmmtoolbox extract sydney_sps.out link,link597,1 link,link597,2 link,link597,3 link,link597,4 >link597
0--flow rate
1--height
2--flow
3-- froud number
4--capacity
in dropdown,
swmmtoolbox listdetail sydney_sps.out node
swmmtoolbox extract sydney_sps.out node,nodeSPS0067,1 >nodeSPS0067_1
0. depth_above_invert
1. hydraulic head
2. volume_storeded_ponded
3.lateral inflow
4. total inflow
5. flow lost_flooding
swmmtoolbox extract sydney_sps.out node,nodeSPS0067,2 node,nodeSPS0067,3 node,nodeSPS0067,4 node,nodeSPS0067,5 >nodeSPS0067_2
Monday, 18 May 2015
Tuesday, 5 May 2015
slurm study
/usr/share/doc/slurm-llnl-doc/
slurm-llnl-doc install
the location is at /usr/share/doc/slurm-llnl-doc/html
http://sphaleron.blogspot.com.au/2011/08/really-super-quick-start-guide-to.html
Really Super Quick Start Guide to Setting Up SLURM
SLURM is the awesomely-named Simple Linux Utility for Resource Management written by the good people at LLNL. It's basically a smart task queuing system for clusters. My cluster has always run Sun Grid Engine, but it looks like SGE is more or less dead in the post-Oracle Sun software apocalypse. In light of this and since SGE recently looked at me the wrong way, I'm hoping to ditch it for SLURM. I like pop culture references and software that works.
The "Super Quick Start Guide" for LLNL SLURM has a lot of words, at least one of which is "make." If you're lazy like me, just do this:
0. Be using Ubuntu
1. Install: # apt-get install slurm-llnl
2. Create key for MUNGE authentication: /usr/sbin/create-munge-key
3a. Make config file: https://computing.llnl.gov/linux/slurm/configurator.html
3b. Put config file in: /etc/slurm-llnl/slurm.conf
4. Start master: # slurmctld
5. Start node: # slurmd
6. Test that fool: $ srun -N1 /bin/hostname
https://paolobertasi.wordpress.com/2011/05/24/how-to-install-slurm-on-debian/
slurm-llnl-doc install
the location is at /usr/share/doc/slurm-llnl-doc/html
http://sphaleron.blogspot.com.au/2011/08/really-super-quick-start-guide-to.html
Really Super Quick Start Guide to Setting Up SLURM
SLURM is the awesomely-named Simple Linux Utility for Resource Management written by the good people at LLNL. It's basically a smart task queuing system for clusters. My cluster has always run Sun Grid Engine, but it looks like SGE is more or less dead in the post-Oracle Sun software apocalypse. In light of this and since SGE recently looked at me the wrong way, I'm hoping to ditch it for SLURM. I like pop culture references and software that works.
The "Super Quick Start Guide" for LLNL SLURM has a lot of words, at least one of which is "make." If you're lazy like me, just do this:
0. Be using Ubuntu
1. Install: # apt-get install slurm-llnl
2. Create key for MUNGE authentication: /usr/sbin/create-munge-key
3a. Make config file: https://computing.llnl.gov/linux/slurm/configurator.html
3b. Put config file in: /etc/slurm-llnl/slurm.conf
4. Start master: # slurmctld
5. Start node: # slurmd
6. Test that fool: $ srun -N1 /bin/hostname
service slurm-llnl restart
cat slurmctld.log
[2015-05-06T13:36:48] Job accounting information stored, but details not gathered
[2015-05-06T13:36:48] error: open /var/log/slurm_jobacct.log: Permission denied
[2015-05-06T13:36:48] error: Couldn't load specified plugin name for accounting_storage/filetxt: Plugin init() callback failed
[2015-05-06T13:36:48] error: cannot resolve acct_storage plugin operations
[2015-05-06T13:36:48] slurmctld version 2.3.2 started on cluster cluster
[2015-05-06T13:36:48] error: open /var/log/slurm_jobacct.log: Permission denied
[2015-05-06T13:36:48] error: Couldn't load specified plugin name for accounting_storage/filetxt: Plugin init() callback failed
[2015-05-06T13:36:48] error: cannot resolve acct_storage plugin operations
[2015-05-06T13:36:48] fatal: failed to initialize accounting_storage plugin
https://paolobertasi.wordpress.com/2011/05/24/how-to-install-slurm-on-debian/
- /etc/init.d/slurm-llnl start
Wednesday, 8 April 2015
git study
git rev-list HEAD --count
put version into git repo
git log --oneline get a list of commited result.
git log --oneline --graph --decorate --all
display the number of commits
put version into git repo
git log --oneline get a list of commited result.
git log --oneline --graph --decorate --all
see the whole tree of the current code.
see [http://stackoverflow.com/questions/5361019/viewing-full-version-tree-in-git]
echo "#define GIT_REF \"`git show-ref refs/heads/master | cut -d " " -f 1 | cut -c 31-40`\"" >
put one line in sutra to demonstrate the version number
[http://stackoverflow.com/questions/2696975/how-do-i-add-revision-and-build-date-to-source]
git checkout 5b01926d4bdc850de431ae3cc1d6098168288826
go to another version. do not worry about the possible update you make, because if you have modification, you checkout will be aborted.
git clean -f examples/ delete all the redundant files
put one line in sutra to demonstrate the version number
[http://stackoverflow.com/questions/2696975/how-do-i-add-revision-and-build-date-to-source]
git checkout 5b01926d4bdc850de431ae3cc1d6098168288826
go to another version. do not worry about the possible update you make, because if you have modification, you checkout will be aborted.
git clean -f examples/ delete all the redundant files
Wednesday, 25 March 2015
segmentation fault
After refining the mesh for p3, the program ends up with segmetation fault.
after debugging using idb, it is found it crashes at a line that writes result into file. apparently it is not casued by this line simply. the problem can be reproduced by using gfortran.
I was suggested by changing the stack size by
ulimit -s 4000000
the way to get around is to compile the source code by windows. at least the program is now working.
case 2
the second time i see segmentation fault is that one of the files are not properly transfered from source to sub functions.
say: call aaa(a,b,c)
in aaa :
aaa(a,b)
c=12
this may cause segmentation fault
after debugging using idb, it is found it crashes at a line that writes result into file. apparently it is not casued by this line simply. the problem can be reproduced by using gfortran.
I was suggested by changing the stack size by
ulimit -s 4000000
the way to get around is to compile the source code by windows. at least the program is now working.
case 2
the second time i see segmentation fault is that one of the files are not properly transfered from source to sub functions.
say: call aaa(a,b,c)
in aaa :
aaa(a,b)
c=12
this may cause segmentation fault
gdb (gefortran --debug) debug
Intel fortran on linux is no longer free, which is annoying as a fortran user. I dicided to change to gfortran instead.
to creat a executable file that can debug, one can use '-g' flag
TBH, at the very beginning, it is quite annoying to use command interface to do the debugging, but
gfortran -g a.F90 -o ab
it is also found that the files has to be compiled by the same compiler in the same machine to ensure the readability of the code.
to creat a executable file that can debug, one can use '-g' flag
TBH, at the very beginning, it is quite annoying to use command interface to do the debugging, but
gfortran -g a.F90 -o ab
1. use gdb (15-06-29) it is also found that the files has to be compiled by the same compiler in the same machine to ensure the readability of the code.
gfortran -ggdb a.f -o a.out
then use the following command to start debug processes.
gdb ab
other useful command:
break main
run [r]
step [s] (step into the subroutine)
print a [p a]
where
quit
next (n) go to the next line without step into subfunctions just over the current
n 5 go to the next for 5 times
next (n) go to the next line without step into subfunctions just over the current
n 5 go to the next for 5 times
2. Info command
info b see all the breaking points info breakpoints check all of the breakpoints
frame display current line
finish stepout
https://www.google.com.au/url?sa=t&rct=j&q=&esrc=s&source=web&cd=5&ved=0CDcQFjAE&url=http%3A%2F%2Fdarkdust.net%2Ffiles%2FGDB%2520Cheat%2520Sheet.pdf&ei=HH4zVZnBO4PsmAXPz4HoCQ&usg=AFQjCNHCDpbVUfxmJyacITfnesZ0PKBKqg&sig2=ImgMp83YjaeYNoztPgTw-w&bvm=bv.91071109,d.dGY&cad=rja
http://stackoverflow.com/questions/501486/getting-gdb-to-save-a-list-of-breakpoints
save breakpoints a.txt
how to load break points --
source a.txt
Error: Dummy argument 'cherin' of procedure 'readif' at (1) has an attribute that requires an explicit interface for this procedure
info line shows where current script is stoped at
delete 1 delete break point 1 from list info b
disable 1
enable 1
disable disable all break points
break sutra.f:333 %stop at line 333 of file sutra.fdelete 1 delete break point 1 from list info b
disable 1
enable 1
disable disable all break points
frame display current line
finish stepout
https://www.google.com.au/url?sa=t&rct=j&q=&esrc=s&source=web&cd=5&ved=0CDcQFjAE&url=http%3A%2F%2Fdarkdust.net%2Ffiles%2FGDB%2520Cheat%2520Sheet.pdf&ei=HH4zVZnBO4PsmAXPz4HoCQ&usg=AFQjCNHCDpbVUfxmJyacITfnesZ0PKBKqg&sig2=ImgMp83YjaeYNoztPgTw-w&bvm=bv.91071109,d.dGY&cad=rja
http://stackoverflow.com/questions/501486/getting-gdb-to-save-a-list-of-breakpoints
save breakpoints a.txt
how to load break points --
source a.txt
Error: Dummy argument 'cherin' of procedure 'readif' at (1) has an attribute that requires an explicit interface for this procedure
set breakpoint pending on
No symbol table is loaded. Use the "file" command.
(1) if something is wrong in the source code. one does not need to quit gdb. instead, just correct the file, make it with debug flag, and rerun simulation in gdb using r.
No symbol table is loaded. Use the "file" command.
2. Correct the program. (15-06-29)(1) if something is wrong in the source code. one does not need to quit gdb. instead, just correct the file, make it with debug flag, and rerun simulation in gdb using r.
- Start the program being debugged.Example 1. The program is printch, which can take an optional command line argument. Start it running with no command line argument.
(gdb)
Example 2. Start printch running with command line argument A.r
(gdb)
r A - Execute a single statement. If the statement is a function call, just single step into the function.
(gdb)
s - Execute a single statement. If the statement is a function call, execute the entire function and return to the statement just after the call; that is, step over the function.
(gdb)
n - Execute from the current point up to the next breakpoint if there is one, otherwise execute until the program terminates.
(gdb)
c - Execute the rest of the current function; that is, step out of the function.
(gdb)
finish
Sunday, 15 February 2015
mflab -- malab read excel using xlsread slow down problem
1. it is the second time i found matlab is doing dodgy things.
Specifically, It is found that mflab in some machines are extremetly slow. the main slow down script
turns out,
line 88 h=feval(['COM.' convertedProgID], 'server', machinename, interface);
at
C:\Program Files\MATLAB\R2012b\toolbox\matlab\winfun\actxserver.m
or
C:\Program Files\MATLAB\R2014a\toolbox\matlab\winfun\actxserver.m
Specifically, It is found that mflab in some machines are extremetly slow. the main slow down script
turns out,
line 88 h=feval(['COM.' convertedProgID], 'server', machinename, interface);
at
C:\Program Files\MATLAB\R2012b\toolbox\matlab\winfun\actxserver.m
or
C:\Program Files\MATLAB\R2014a\toolbox\matlab\winfun\actxserver.m
is the problematic file. just change it into
line 88 h=feval([convertedProgID], 'server', machinename, interface);
solves the slow down problem
2. aera object not working.
2015-02-16 change fdm3.m file into the old one will make area object working
1. et doesn't work, no matter how many time i have checked the input.
solution. reboot matlab, and use mflab in southern folder.
10/03/15
rect_2 is designed to make very small et and start from low, now i am trying to make et very low at the beginning.
apparently the flow one does not work at all!!!
There is a tricky part for the volumetric flow given by budget, particularly at the cell where water table locates. the front or right side flux is not calculated by volumetric flow on cross section area of the cell, but volumetric flow on wetting area of the CELL!!!
Comment 1: if there is only one layer of cell, the first layer SHOULD be set as unconfied rather than varying cells. so that the result is correct. a experience from changing one layer from modflow_no_leak
and modflow_rect_dd_1
Comment 2: if the time-variant specified head is not working properly, particularly the cells above the time variant hydraulic head is not wetted again, one should always make sure the cell abve the manipulated cell wet. This can be done either by moving the manipulated cell downward, or change the bottom hydraulic head that is manipulating.
example study:
mf2005\TerwisschaPE lots of stress periods. theis equation is considered
mf2005\DutchTop\RainLens very good chd package, but the simulation is not working. needs to find out the way to get it running. perhaps git back to the previous versions.
an further analyze has indicated that mf2005 is performing better than mf2000 in terms of handling wetting and drying functions. specifically when WETDRY is positive, meaning cells from all directions can make the dry cell rewetted, mf2005 is able to deliver nice results while mf2000 can not get converged.
*** ERROR OPENING FILE "Q2.HDS" ON UNIT 51
SPECIFIED FILE STATUS: UNKNOWN
SPECIFIED FILE FORMAT: BINARY
SPECIFIED FILE ACCESS: SEQUENTIAL
SPECIFIED FILE ACTION: READWRITE
-- STOP EXECUTION (SGWF2BAS7OPEN)
solution:
1. download modflow for unix (
2. in openspec.inc, comment DATA FORM/'BINARY'/ and uncomment DATA FORM/'UNFORMATTED'/.
3. make the binary file
mf2kgmg.h: In function ‘MF2KGMG_BIGH’:
mf2kgmg.h:448:29: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
pcgn2.f90:26.6:
USE PCG_MAIN
1
Fatal Error: Can't open module file 'pcg_main.mod' for reading at (1): No such file or directory
utl7.f:234.14:
IF ( LVAL.EQ. .FALSE. ) THEN
1
Error: Logicals at (1) must be compared with .eqv. instead of .eq.
utl7.f:263.14:
IF ( LVAL.EQ. .FALSE. ) THEN
1
Error: Logicals at (1) must be compared with .eqv. instead of .eq.
(1) improve quiver object
$ grep -r -i --include *.m quiver ~/Projects/mflab/trunk/examples/
/home/chenming/Projects/mflab/trunk/examples/Analytic/GGOR/Analytic04.m:if isphi==0 % if averag seepage from second aquiver is given
/home/chenming/Projects/mflab/trunk/examples/mf2k/Qanats/TafiletMdl/mfiles/mf_analyze.m:%gr.quiver(B,1,'k','power',0.5);
/home/chenming/Projects/mflab/trunk/examples/mf2k/Qanats/TafiletMdl/SCENARIOS/mf_analyze.m:%gr.quiver(B,1,'k','power',0.5);
1. et doesn't work, no matter how many time i have checked the input.
solution. reboot matlab, and use mflab in southern folder.
10/03/15
rect_2 is designed to make very small et and start from low, now i am trying to make et very low at the beginning.
apparently the flow one does not work at all!!!
There is a tricky part for the volumetric flow given by budget, particularly at the cell where water table locates. the front or right side flux is not calculated by volumetric flow on cross section area of the cell, but volumetric flow on wetting area of the CELL!!!
Comment 1: if there is only one layer of cell, the first layer SHOULD be set as unconfied rather than varying cells. so that the result is correct. a experience from changing one layer from modflow_no_leak
and modflow_rect_dd_1
Comment 2: if the time-variant specified head is not working properly, particularly the cells above the time variant hydraulic head is not wetted again, one should always make sure the cell abve the manipulated cell wet. This can be done either by moving the manipulated cell downward, or change the bottom hydraulic head that is manipulating.
example study:
mf2005\TerwisschaPE lots of stress periods. theis equation is considered
mf2005\DutchTop\RainLens very good chd package, but the simulation is not working. needs to find out the way to get it running. perhaps git back to the previous versions.
an further analyze has indicated that mf2005 is performing better than mf2000 in terms of handling wetting and drying functions. specifically when WETDRY is positive, meaning cells from all directions can make the dry cell rewetted, mf2005 is able to deliver nice results while mf2000 can not get converged.
*** ERROR OPENING FILE "Q2.HDS" ON UNIT 51
SPECIFIED FILE STATUS: UNKNOWN
SPECIFIED FILE FORMAT: BINARY
SPECIFIED FILE ACCESS: SEQUENTIAL
SPECIFIED FILE ACTION: READWRITE
-- STOP EXECUTION (SGWF2BAS7OPEN)
solution:
1. download modflow for unix (
2. in openspec.inc, comment DATA FORM/'BINARY'/ and uncomment DATA FORM/'UNFORMATTED'/.
3. make the binary file
mf2kgmg.h:448:29: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
pcgn2.f90:26.6:
USE PCG_MAIN
1
Fatal Error: Can't open module file 'pcg_main.mod' for reading at (1): No such file or directory
utl7.f:234.14:
IF ( LVAL.EQ. .FALSE. ) THEN
1
Error: Logicals at (1) must be compared with .eqv. instead of .eq.
utl7.f:263.14:
IF ( LVAL.EQ. .FALSE. ) THEN
1
Error: Logicals at (1) must be compared with .eqv. instead of .eq.
(1) improve quiver object
$ grep -r -i --include *.m quiver ~/Projects/mflab/trunk/examples/
/home/chenming/Projects/mflab/trunk/examples/Analytic/GGOR/Analytic04.m:if isphi==0 % if averag seepage from second aquiver is given
/home/chenming/Projects/mflab/trunk/examples/mf2k/Qanats/TafiletMdl/mfiles/mf_analyze.m:%gr.quiver(B,1,'k','power',0.5);
/home/chenming/Projects/mflab/trunk/examples/mf2k/Qanats/TafiletMdl/SCENARIOS/mf_analyze.m:%gr.quiver(B,1,'k','power',0.5);
samba share
For file linux file system applying on windows, it is always the best to use samba share.
The confiuration file is given as follows:
1. uncommet the follow line in /etc/samba/smb.conf
2. creater new users by
3. restart samba process by:
The confiuration file is given as follows:
1. uncommet the follow line in /etc/samba/smb.conf
#======================= Share Definitions ======================= # Un-comment the following (and tweak the other settings below to suit) # to enable the default home directory shares. This will share each # user's home director as \\server\username [homes] comment = Home Directories browseable = no
2. creater new users by
#smbpasswd -a chenming
#systemctl restart smbd #systemctl restart nmbd
4. test the connections by:
#smbclient -L localhost
once there is an error
ae429-1105 chenming # smbclient -L 10.33.20.12X Enter root's password: Connection to 10.33.20.120 failed (Error NT_STATUS_CONNECTION_REFUSED)
the problem is solved by restart samba
5. now it is time to mouprint(gcf,'-dpng',sprintf('-r%d',r), 'bar.png');nt the samba share by right click My computer -> map networkdrive->\\10.33.20.120\chenming and then password
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