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class=234111511-10122008>reply at bottom of mail
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<DIV>> poos001@D0400736:~/admb$ export
ADMB_HOME=/home/poos001/admb-9.0.65-linux64-gcc3.4.6/<BR><BR>remove the trailing
backslash, so that<BR>$ export
ADMB_HOME=/home/poos001/admb-9.0.65-linux64-gcc3.4.6<BR><BR>then <BR>$ export
PATH=$ADMB_HOME/bin:$PATH<BR><BR>finally<BR>$ tpl2rem envpref<BR><BR>let me
know,<BR>johnoel<BR>----- Original Message -----<BR>From: "Poos, Jan Jaap"
<janjaap.Poos@wur.nl><BR>Date: Tuesday, December 9, 2008 10:49
pm<BR>Subject: Re: [ADMB Users] glitch in tpl2rem (and tpl2cpp) ?<BR>To:
users@admb-project.org<BR><BR>> <BR>> My reply is at
bottom...<BR>> <BR>> -----Original Message-----<BR>> From:
users-bounces@admb-project.org [mailto:users-bounces@admb-<BR>> project.org]
On Behalf Of John Ancheta<BR>> Sent: Tuesday, December 09, 2008 7:37
PM<BR>> To: users@admb-project.org<BR>> Subject: Re: [ADMB Users] glitch
in tpl2rem (and tpl2cpp) ?<BR>> <BR>> Download and install a current
version of ADMB from<BR>> <BR>> http://admb-project.org/downloads<BR>>
<BR>> Installation guides can be found at<BR>> <BR>>
http://admb-project.org/documentation<BR>> <BR>> Let me know,<BR>>
johnoel<BR>> <BR>> On Dec 9, 5:53 am, "Poos, Jan Jaap"
<janjaap.P...@wur.nl> wrote:<BR>> > Hi,<BR>> ><BR>> > I
found a small problem with respect to tpl2rem on linux, <BR>> using <BR>>
> admb-9.0.9rc2-linux64-gcc3.4. When using tpl2rem on a file on <BR>> one
of <BR>> > our network disks, this results in:<BR>> ><BR>> >
sh: envpref.htp: Permission denied<BR>> > Error executing command
sed -e " " classdef.tmp > envpref.htp<BR>> > sh:
envpref.htp: Permission denied<BR>> > Error executing command sed -n
-f<BR>> > /home/poos001/admb-9.0.9rc2-linux64-gcc3.4/bin<BR>> >
/seddf1b3 tfile2 >> envpref.htp<BR>> > sh: envpref.htp: Permission
denied<BR>> > Error executing command sed -n -f<BR>> >
/home/poos001/admb-9.0.9rc2-linux64-gcc3.4/bin<BR>> > /seddf1b4 tfile4
>> envpref.htp<BR>> > sh: envpref.htp: Permission denied<BR>>
> Error executing command sed -f<BR>> >
/home/poos001/admb-9.0.9rc2-linux64-gcc3.4/bin/se<BR>> > ddf1b2 tfile2
>> envpref.htp<BR>> > etc.<BR>> ><BR>> > Subsequently,
the directory in which the tpl file is located <BR>> looks like:<BR>>
><BR>> > -rw-r--r-- 1 root imares 1894
2008-12-09 16:36 classdef.tmp<BR>> > -rw-r--r-- 1 root imares
3817 2008-12-09 16:36 <BR>> envpref.cpp <BR>> > -rwxrwxrwx
1 poos001 imares 6622965 2008-10-04 22:25 envpref.dat<BR>> > -rw-r--r-- 1
root imares 1894 2008-12-09 16:36 <BR>> envpref.htp
<BR>> > -rwxrwxrwx 1 poos001 imares 4132 2008-10-04 22:25
<BR>> envpref.pin <BR>> > -rwxrwxrwx 1 poos001 imares 2308
2008-12-09 14:01 envpref.tpl<BR>> > -rw-r--r-- 1 root imares
0 2008-12-09 16:36 header.tmp<BR>> > -rw-r--r-- 1
root imares 1263 2008-12-09 16:36 tfile1<BR>> >
-rw-r--r-- 1 root imares 126 2008-12-09 16:36
tfile2<BR>> > -rw-r--r-- 1 root imares 383
2008-12-09 16:36 tfile3<BR>> > -rw-r--r-- 1 root imares
122 2008-12-09 16:36 tfile4<BR>> > -rw-r--r-- 1 root
imares 585 2008-12-09 16:36 xxalloc1.tmp<BR>> >
-rw-r--r-- 1 root imares 179 2008-12-09 16:36
xxalloc2.tmp<BR>> > -rw-r--r-- 1 root imares
836 2008-12-09 16:36 <BR>> xxalloc3.tmp <BR>> > -etc.<BR>>
><BR>> > So, all the temporary files remain in the directory. Running
<BR>> tpl2rem <BR>> > again results in a segmentation fault.<BR>>
><BR>> > This looks like a problem with setting the permissions when
<BR>> the <BR>> > temporary files are made. The problem disappears when
copying <BR>> the <BR>> > files to another location (like the users
home dir). The same <BR>> problem <BR>> > also disappears when running
tpl2env as root. Maybe this can <BR>> be looked <BR>> > into and fixed
in a future version?<BR>> ><BR>> > Cheers, thanks in advance, Jan
Jaap<BR>> ><BR>> >
_______________________________________________<BR>> > Users mailing
list<BR>> > Us...@admb-project.orghttp://lists.admb-<BR>>
project.org/mailman/listinfo/u> sers<BR>>
_______________________________________________<BR>> Users mailing
list<BR>> Users@admb-project.org<BR>>
http://lists.admb-project.org/mailman/listinfo/users<BR>> <BR>> Hi
John,<BR>> <BR>> Thanks for your swift reaction. However, it appears the
problem <BR>> is not fixed, but has become worse. With v 9.0.65, tpl2rem
fails <BR>> also in a situation where it worked previously:<BR>> <BR>>
poos001@D0400736:~/admb$ export ADMB_HOME=/home/poos001/admb-<BR>>
9.0.65-linux64-gcc3.4.6/<BR>> poos001@D0400736:~/admb$ ./tpl2rem
envpref<BR>> sed: couldn't open file
/home/poos001/admb-9.0.65-linux64-<BR>> gcc3.4.6/binseddf1b3: No such file or
directory<BR>> Error executing command sed -n -f
/home/poos001/admb-9.0.65-<BR>> linux64-gcc3.4.6/binseddf1b3 tfile2 >>
envpref.htp<BR>> sed: couldn't open file
/home/poos001/admb-9.0.65-linux64-<BR>> gcc3.4.6/binseddf1b4: No such file or
directory<BR>> Error executing command sed -n -f
/home/poos001/admb-9.0.65-<BR>> linux64-gcc3.4.6/binseddf1b4 tfile4 >>
envpref.htp<BR>> sed: couldn't open file
/home/poos001/admb-9.0.65-linux64-<BR>> gcc3.4.6/binseddf1b2: No such file or
directory<BR>> Error executing command sed -f
/home/poos001/admb-9.0.65-linux64-<BR>> gcc3.4.6/binseddf1b2 tfile2 >>
envpref.htp<BR>> sed: couldn't open file
/home/poos001/admb-9.0.65-linux64-<BR>> gcc3.4.6/binsedf1b2d: No such file or
directory<BR>> Error executing command sed -f
/home/poos001/admb-9.0.65-linux64-<BR>> gcc3.4.6/binsedf1b2d tfile4 >>
envpref.htp<BR>> sed: couldn't open file
/home/poos001/admb-9.0.65-linux64-<BR>> gcc3.4.6/binsedf1b2a: No such file or
directory<BR>> Error executing command sed -f
/home/poos001/admb-9.0.65-linux64-<BR>> gcc3.4.6/binsedf1b2a xxalloc3.tmp
>> envpref.cpp<BR>> sed: couldn't open file
/home/poos001/admb-9.0.65-linux64-<BR>> gcc3.4.6/binsedf1b2c: No such file or
directory<BR>> Error executing command sed -f
/home/poos001/admb-9.0.65-linux64-<BR>> gcc3.4.6/binsedf1b2c xxalloc2.tmp
>> envpref.cpp<BR>> Error trying to create output file
envpref.cpp<BR>> <BR>> It appears the forward slash between bin and the
sed files has <BR>> disappeared, resulting in similar issues as before, only
now in <BR>> all instances. Mind you I use x86_64 and gcc 4.3.1, with the
<BR>> files for gcc3.4.6, but I don't think this is the issue. <BR>>
<BR>> All the files in admb-9.0.65-linux64-gcc3.4.6/bin are owned by <BR>>
poos001, and have -rwxrwxrwx permission.<BR>> <BR>> Kind regards, Jan
Jaap <BR><SPAN class=234111511-10122008><FONT face=Arial
color=#0000ff size=2> </FONT></SPAN></DIV>
<DIV><SPAN class=234111511-10122008><FONT face=Arial color=#0000ff
size=2>-------------</FONT></SPAN></DIV>
<DIV><SPAN class=234111511-10122008><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=234111511-10122008><FONT face=Arial color=#0000ff
size=2>Removing the trailing slash from ADMB_HOME and explicitly adding
$ADMB_HOME/bin to the path did indeed return the behaviour of tpl2rem as
previously. This means it is still not able to properly function at the
specified location. Running tpl2rem results in:</FONT></SPAN></DIV>
<DIV><SPAN class=234111511-10122008><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=234111511-10122008><FONT face=Arial color=#0000ff size=2><A
href="mailto:poos001@D0400736:/media/n/Projecten/Computing">poos001@D0400736:/media/n/Projecten/Computing</A>
desktop Texel/admb$ export PATH=$ADMB_HOME/bin:$PATH<BR><A
href="mailto:poos001@D0400736:/media/n/Projecten/Computing">poos001@D0400736:/media/n/Projecten/Computing</A>
desktop Texel/admb$ ./tpl2rem envpref<BR>sh: envpref.htp: Permission
denied<BR>Error executing command sed -e " " classdef.tmp >
envpref.htp<BR>sh: envpref.htp: Permission denied<BR>Error executing command sed
-n -f /home/poos001/admb-9.0.65-linux64-gcc3.4.6/bin/seddf1b3 tfile2 >>
envpref.htp<BR>sh: envpref.htp: Permission denied<BR></FONT></SPAN><SPAN
class=234111511-10122008><FONT face=Arial color=#0000ff
size=2>etc.</FONT></SPAN></DIV>
<DIV><SPAN class=234111511-10122008><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=234111511-10122008><FONT face=Arial color=#0000ff size=2>he
problem is that envpref is owned by root, and does not get write permissions by
anybody else but root: </FONT></SPAN></DIV>
<DIV><SPAN class=234111511-10122008><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=234111511-10122008><FONT face=Arial color=#0000ff size=2>ls -la
envpref.htp results in:</FONT></SPAN></DIV><SPAN class=234111511-10122008><FONT>
<DIV><FONT face=Arial color=#0000ff size=2></FONT> </DIV>
<DIV><FONT face=Arial color=#0000ff size=2>-rw-r--r-- 1 root
imares 1894 2008-12-10 13:18 envpref.htp<BR></FONT></DIV>
<DIV><SPAN class=234111511-10122008><FONT face=Arial color=#0000ff size=2>Thus,
appending of the results of sed (that is done by poos001) cannot be
done because poos001 does not have permission to write the file. The
problem could be solved by making sure that envpref.htp and envpref.cpp get
permission -rw-rw-rw- when they are created. Alternatively, the .cpp and
.htp file can be created somewhere differently and copied into the
directory in one go. I realize this problem is partly the result of our
hardware and using smbfs. That results in the owner of the file being
"root" and not the
current user. </FONT></SPAN></DIV></FONT></SPAN>
<DIV><SPAN class=234111511-10122008></SPAN><SPAN class=234111511-10122008><FONT
face=Arial color=#0000ff size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=234111511-10122008><FONT face=Arial color=#0000ff
size=2>Cheers, Jan Jaap </FONT></SPAN></DIV>
<DIV><SPAN class=234111511-10122008><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
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