<div dir="ltr">Hi,<br> I also had a bit of a struggle installing SHARP on Ubuntu, (Hardy Heron currently, but Gutsy also previously), but got it working eventually.<br><br>The default httpd binary core dumped, but the answer for me was to move the httpd binary (unpacked from "helpers_server.linux.tar.gz") to somewhere else, then use the httpd.SuSE-9.3 binary <br>
e.g.:<br><br>%mv httpd httpd.distrib<br>%mv httpd.SuSE-9.3 httpd<br><br>...then use the kill_server/restart_server scripts to start the server.<br>I have Sharp running on port 8080, and the vanilla Apache2 from Ubuntu running on 80, and they don't get in the way of each other.<br>
<br>I guess that recompiling either Apache2 or Apache 1.3.X is overkill, and instead you should concentrate on getting the available Apache 1.3 binaries distributed with SHARP to run. I don't have access to the machine in question right now, but I think that Apache should give a logfile when it dies. <br>
<br>Good luck,<br><br>Mark <br> <br><br><div class="gmail_quote">2008/8/15 <span dir="ltr"><<a href="mailto:sharp-discuss-request@globalphasing.com" target="_blank">sharp-discuss-request@globalphasing.com</a>></span><br>
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Today's Topics:<br>
<br>
1. Re: apache2 not starting on Ubuntu 7.04 SHARP installation<br>
(Lee S Parsons)<br>
2. Re: apache2 not starting on Ubuntu 7.04 SHARP installation<br>
(Clemens Vonrhein)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Thu, 14 Aug 2008 12:33:08 -0400<br>
From: Lee S Parsons <<a href="mailto:parsonsl@upstate.edu" target="_blank">parsonsl@upstate.edu</a>><br>
Subject: Re: [sharp-discuss] apache2 not starting on Ubuntu 7.04 SHARP<br>
installation<br>
To: Clemens Vonrhein <<a href="mailto:vonrhein@globalphasing.com" target="_blank">vonrhein@globalphasing.com</a>><br>
Cc: <a href="mailto:sharp-discuss@globalphasing.com" target="_blank">sharp-discuss@globalphasing.com</a><br>
Message-ID: <<a href="mailto:48A45E44.4020300@upstate.edu" target="_blank">48A45E44.4020300@upstate.edu</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Dr. Vonrhein<br>
<br>
Thank you for your reply, here is an update:<br>
<br>
Clemens Vonrhein wrote:<br>
><br>
> You should be able to create new users for the SHARP server by doing:<br>
><br>
> % cd /where/ever/sharp<br>
> % source ./setup.csh # tcsh/csh<br>
> - or -<br>
> % . ./setup.sh # sh/bash/ksh/zsh<br>
> % adm/bin/newuser<br>
><br>
><br>
<br>
<br>
I should have mentioned, I was able to create new users using the<br>
newuser script, but I could never log in as them. Only the user that I<br>
created when setting up SHARP was allowed in.<br>
<br>
<br>
><br>
> % cd /where/ever/sharp<br>
> % source ./setup.csh # tcsh/csh<br>
> - or -<br>
> % . ./setup.sh # sh/bash/ksh/zsh<br>
> % adm/bin/kill_server<br>
> % adm/bin/restart_server<br>
> % adm/bin/check_server<br>
><br>
><br>
<br>
As mentioned, restart_server (sorry about the earlier typo) dies<br>
immediately with the "AuthUserFile" error that I mentioned earlier.<br>
Still trying to figure out how to get around that one...<br>
<br>
Though kill_server is now irrelevant, since the server doesn't start at<br>
all since the reboot...<br>
<br>
><br>
> You are trying to use apache2 as the httpd for SHARP/autoSHARP? This<br>
> is different from the recommended version of the apache httpd (1.3.X)<br>
> that also comes with the SHARP/autoSHARP files<br>
> (helpers_server.*.tar.gz). There is a basic example configuration file<br>
> for apache2 available in $BDG_home/sushi/conf, but this might need<br>
> some tweaking and editing before it is going to work.<br>
><br>
><br>
<br>
Maybe I misread the installation information on the SHARP website - I<br>
thought I had to install Apache before installing SHARP.<br>
<br>
<br>
> If at all possible, try to use the 1.3.X httpd binary that comes as<br>
> part of the installation. Or compile your own 1.3.X binary - for<br>
> details see $BDG_home/helpers/*/httpd.README_GPhL on how to do that.<br>
><br>
><br>
<br>
I just tried starting the 1.3.34 that came with SHARP - I extracted the<br>
contents of the tarball into /usr/local/Helpers-server/ (notice the<br>
intentional capitalization). I then tried<br>
<br>
/usr/local/Helpers-server/httpd -f<br>
/usr/local/SHARP/sushi/conf/httpd-1.3.conf<br>
<br>
And the response was a core dump.<br>
<br>
<br>
> If you are using a apache httpd binary coming with your operating<br>
> system: be aware that these are very often compiled/configured<br>
> differently from a plain default installation of the official Apache<br>
> httpd distribution. OS supplier configure their version of the Apache<br>
> httpd very modular which would require that you have to manually load<br>
> all kind of modules before it will behave as expected by<br>
> SHARP/autoSHARP (which assumes a httpd installation based on the<br>
> official Apache httpd distribution).<br>
><br>
><br>
I think I have the modules part figured out - it seems that there is a<br>
syntax problem somewhere in here that involves the difference in<br>
configurations between Apache 1.3.x and 2.2.x. I verified which<br>
modules to run for Apache2 (and we even had it somehow working right<br>
after the SHARP install - just never again).<br>
<br>
<br>
<br>
<br>
> 2 possibilities (with 2 sub-possibilities each):<br>
><br>
> 1. use a 1.3.X version of the httpd<br>
><br>
> a) we do ship pre-compiled binaries inside of<br>
> helpers_server.*.tar.gz that can be tried<br>
><br>
<br>
I've tried them, and found that:<br>
( .RedHat-FC3, .glibc23, .SuSE-9.1, .SuSE-9.3) return an error on not<br>
being able to resolve the FQDN, and then promptly die without leaving<br>
any messages<br>
<br>
( .RedHat-7.3, .glibc22, and "httpd" with nothing after it) all segfault<br>
and core dump.<br>
<br>
This was when using the config file at<br>
/usr/local/SHARP/sushi/conf/httpd-1.3.conf<br>
<br>
<br>
> b) if none of those works (because of the way the httpd is built<br>
> this can happen): just follow the instructions in<br>
> /usr/local/SHARP/helpers/*/httpd.README_GPhL to compile your<br>
> own (very easy). This is then guaranteed to work on that<br>
> machine.<br>
><br>
><br>
<br>
When I opened the tarball "helpers_server.linux.tar.gz", there was no<br>
file "apache_1.3.34.tar.gz" as suggested by httpd.README_GPhL. Should I<br>
download that version directly from the Apache group and build it myself?<br>
<br>
<br>
<br>
<br>
> 2. use a 2.X version of the httpd: you will most likely need to do<br>
> some editing in the configuraiton file.<br>
><br>
><br>
> a) try using the system-supplied apache2 binary: you need to load<br>
> additional modules ... but I don't know which (depends on your<br>
> operating system and how the vendor has configured it)<br>
><br>
><br>
<br>
It seems like the problem lies in how the "AuthUserFile" method is<br>
called. I'm looking to see if I can find good documentation on how it<br>
may have changed between apache 1.3.x and 2.2.x. I am starting to<br>
wonder if perhaps "AuthUserFile" may have been deprecated (in name)<br>
along the way and replaced by something else.<br>
<br>
> b) compile your own 2.X version<br>
><br>
> I would definitely go with option 1 (hopefully a) but b) is easy<br>
> enough as well). Yes, 1.3.X is a bit older version, but this is a<br>
> httpd running on a local machine on a non-privileged port (8080) under<br>
> a non-root account (right?) behind a firewall (I guess) ... so I can't<br>
> really see any security implications here.<br>
><br>
><br>
><br>
<br>
As much as I didn't think I'd be saying this, we aren't really much at<br>
all concerned about security on this system. You are correct that it is<br>
behind a firewall, running as a non-root account. Apache2 was built<br>
just because this system had no webserver on it prior, so it seemed<br>
logical at the time to build the newest version. We certainly didn't<br>
expect to walk into this mess with the Apache2 config files, or we would<br>
have built the older version instead.<br>
<br>
Any insight on where to go next with this would be great.<br>
<br>
thank you<br>
Lee<br>
<br>
<br>
<br>
> Hope that helps.<br>
><br>
> Cheers<br>
><br>
> Clemens<br>
><br>
><br>
>> thank you<br>
>> Lee Parsons<br>
>> Biochemistry & Molecular Biology<br>
>> SUNY Upstate Medical University<br>
>> Syracuse, NY<br>
>><br>
>><br>
>> _______________________________________________<br>
>> sharp-discuss mailing list<br>
>> <a href="mailto:sharp-discuss@globalphasing.com" target="_blank">sharp-discuss@globalphasing.com</a><br>
>> <a href="https://www.globalphasing.com/mailman/listinfo/sharp-discuss" target="_blank">https://www.globalphasing.com/mailman/listinfo/sharp-discuss</a><br>
>><br>
><br>
><br>
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<br>
Message: 2<br>
Date: Thu, 14 Aug 2008 18:31:15 +0100<br>
From: Clemens Vonrhein <<a href="mailto:vonrhein@globalphasing.com" target="_blank">vonrhein@globalphasing.com</a>><br>
Subject: Re: [sharp-discuss] apache2 not starting on Ubuntu 7.04 SHARP<br>
installation<br>
To: Lee S Parsons <<a href="mailto:parsonsl@upstate.edu" target="_blank">parsonsl@upstate.edu</a>><br>
Cc: <a href="mailto:sharp-discuss@globalphasing.com" target="_blank">sharp-discuss@globalphasing.com</a><br>
Message-ID: <<a href="mailto:20080814173115.GU27765@nx1.globalphasing.com" target="_blank">20080814173115.GU27765@nx1.globalphasing.com</a>><br>
Content-Type: text/plain; charset=us-ascii<br>
<br>
Dear Lee,<br>
<br>
On Thu, Aug 14, 2008 at 12:33:08PM -0400, Lee S Parsons wrote:<br>
>> You should be able to create new users for the SHARP server by doing:<br>
>><br>
>> % cd /where/ever/sharp<br>
>> % source ./setup.csh # tcsh/csh<br>
>> - or -<br>
>> % . ./setup.sh # sh/bash/ksh/zsh<br>
>> % adm/bin/newuser<br>
>><br>
>><br>
><br>
><br>
> I should have mentioned, I was able to create new users using the newuser<br>
> script, but I could never log in as them. Only the user that I created<br>
> when setting up SHARP was allowed in.<br>
<br>
I see. the problem then is probably that the email that should have<br>
been sent out by this 'newuser' command didn't get to them? Often,<br>
email isn't setup on the machine you're running SHARP/autoSHARP. But<br>
the email is actually also saved in<br>
<br>
$BDG_home/users/USERNAME<br>
<br>
so you can have a look at it. The important bit is that every newly<br>
created user needs to run the useSHARP script. It's quite simple:<br>
he/she needs to run<br>
<br>
% /where/ever/sharp/bin/useSHARP USERNAME<br>
<br>
<br>
(where USERNAME is the SHARP username given when running the 'newuser'<br>
script).<br>
<br>
>> % cd /where/ever/sharp<br>
>> % source ./setup.csh # tcsh/csh<br>
>> - or -<br>
>> % . ./setup.sh # sh/bash/ksh/zsh<br>
>> % adm/bin/kill_server<br>
>> % adm/bin/restart_server<br>
>> % adm/bin/check_server<br>
>><br>
>><br>
><br>
> As mentioned, restart_server (sorry about the earlier typo) dies<br>
> immediately with the "AuthUserFile" error that I mentioned earlier. Still<br>
> trying to figure out how to get around that one...<br>
<br>
It's all related to you using a 2.X version of the Apache httpd<br>
distributed by the OS supplier (I'm prettu sure about that).<br>
<br>
> Though kill_server is now irrelevant, since the server doesn't start at all<br>
> since the reboot...<br>
<br>
True: but sometimes the server can't be restarted because th httpd.pid<br>
file of a dead instance is still lurking around. Then the<br>
'kill_server' command is the easiest way of getting rid of it.<br>
<br>
>> You are trying to use apache2 as the httpd for SHARP/autoSHARP? This<br>
>> is different from the recommended version of the apache httpd (1.3.X)<br>
>> that also comes with the SHARP/autoSHARP files<br>
>> (helpers_server.*.tar.gz). There is a basic example configuration file<br>
>> for apache2 available in $BDG_home/sushi/conf, but this might need<br>
>> some tweaking and editing before it is going to work.<br>
>><br>
>><br>
><br>
> Maybe I misread the installation information on the SHARP website - I<br>
> thought I had to install Apache before installing SHARP.<br>
<br>
This might have been unclear: we do supply a pre-compield Apache 1.3.X<br>
httpd binary that _should_ work out of the box (and running<br>
'installSHARP -F' will automatically try using it). If it doesn't work<br>
right away, then the recommendation is to install a fresh 1.3.X<br>
version according to the README file mentioned.<br>
<br>
>> If at all possible, try to use the 1.3.X httpd binary that comes as<br>
>> part of the installation. Or compile your own 1.3.X binary - for<br>
>> details see $BDG_home/helpers/*/httpd.README_GPhL on how to do that.<br>
>><br>
>><br>
><br>
> I just tried starting the 1.3.34 that came with SHARP - I extracted the<br>
> contents of the tarball into /usr/local/Helpers-server/ (notice the<br>
> intentional capitalization).<br>
<br>
You should install it into $BDG_home too as part of the 'installSHARP<br>
-F'. You can in principle install it into a different directory, but<br>
that is just making your life difficult I guess.<br>
<br>
> I then tried<br>
><br>
> /usr/local/Helpers-server/httpd -f<br>
> /usr/local/SHARP/sushi/conf/httpd-1.3.conf<br>
><br>
> And the response was a core dump.<br>
<br>
Yes.<br>
<br>
>> If you are using a apache httpd binary coming with your operating<br>
>> system: be aware that these are very often compiled/configured<br>
>> differently from a plain default installation of the official Apache<br>
>> httpd distribution. OS supplier configure their version of the Apache<br>
>> httpd very modular which would require that you have to manually load<br>
>> all kind of modules before it will behave as expected by<br>
>> SHARP/autoSHARP (which assumes a httpd installation based on the<br>
>> official Apache httpd distribution).<br>
>><br>
>><br>
> I think I have the modules part figured out - it seems that there is a<br>
> syntax problem somewhere in here that involves the difference in<br>
> configurations between Apache 1.3.x and 2.2.x. I verified which modules<br>
> to run for Apache2 (and we even had it somehow working right after the<br>
> SHARP install - just never again).<br>
<br>
Good - if you get it to work with your OS-supplied apache2 binary and<br>
a configuration file in $BDG_home/sushi/conf I'm impressed. I never<br>
bothered, because using a plain 1.3.X is just much easier.<br>
<br>
>> 2 possibilities (with 2 sub-possibilities each):<br>
>><br>
>> 1. use a 1.3.X version of the httpd<br>
>><br>
>> a) we do ship pre-compiled binaries inside of<br>
>> helpers_server.*.tar.gz that can be tried<br>
>><br>
><br>
> I've tried them, and found that:<br>
> ( .RedHat-FC3, .glibc23, .SuSE-9.1, .SuSE-9.3) return an error on not being<br>
> able to resolve the FQDN, and then promptly die without leaving any<br>
> messages<br>
<br>
If you want to test different httpd binaries you need to do this<br>
through the 'httpd-setup' admin tool. So running the sequence<br>
<br>
% adm/bin/kill_server # just in case<br>
% adm/bin/httpd-setup # and pick the httpd and conf file you want<br>
# to use<br>
% adm/bin/restart_server<br>
% adm/bin/check_server<br>
% ps -efl | egrep "httpd|apache2" # just in case<br>
<br>
will show you if the combination of httpd binary and configuration<br>
file is working.<br>
<br>
> ( .RedHat-7.3, .glibc22, and "httpd" with nothing after it) all segfault<br>
> and core dump.<br>
> This was when using the config file at<br>
> /usr/local/SHARP/sushi/conf/httpd-1.3.conf<br>
><br>
><br>
>> b) if none of those works (because of the way the httpd is built<br>
>> this can happen): just follow the instructions in<br>
>> /usr/local/SHARP/helpers/*/httpd.README_GPhL to compile your<br>
>> own (very easy). This is then guaranteed to work on that<br>
>> machine.<br>
>><br>
>><br>
><br>
> When I opened the tarball "helpers_server.linux.tar.gz", there was no file<br>
> "apache_1.3.34.tar.gz" as suggested by httpd.README_GPhL. Should I<br>
> download that version directly from the Apache group and build it myself?<br>
<br>
Yes - and you can download the latest from the 1.3.X series.<br>
<br>
This option is by far the safest for getting everything to work!<br>
<br>
>> 2. use a 2.X version of the httpd: you will most likely need to do<br>
>> some editing in the configuraiton file.<br>
>><br>
>> a) try using the system-supplied apache2 binary: you need to load<br>
>> additional modules ... but I don't know which (depends on your<br>
>> operating system and how the vendor has configured it)<br>
>><br>
>><br>
><br>
> It seems like the problem lies in how the "AuthUserFile" method is called.<br>
> I'm looking to see if I can find good documentation on how it may have<br>
> changed between apache 1.3.x and 2.2.x. I am starting to wonder if perhaps<br>
> "AuthUserFile" may have been deprecated (in name) along the way and<br>
> replaced by something else.<br>
<br>
I think it is a module that needs to be enabled. Apache2 is much more<br>
modular by default _and_ the OS supplier are keen on modular httpds<br>
...<br>
<br>
>> b) compile your own 2.X version<br>
>><br>
>> I would definitely go with option 1 (hopefully a) but b) is easy<br>
>> enough as well). Yes, 1.3.X is a bit older version, but this is a<br>
>> httpd running on a local machine on a non-privileged port (8080) under<br>
>> a non-root account (right?) behind a firewall (I guess) ... so I can't<br>
>> really see any security implications here.<br>
>><br>
>><br>
>><br>
><br>
> As much as I didn't think I'd be saying this, we aren't really much at all<br>
> concerned about security on this system. You are correct that it is behind<br>
> a firewall, running as a non-root account. Apache2 was built just because<br>
> this system had no webserver on it prior, so it seemed logical at the time<br>
> to build the newest version. We certainly didn't expect to walk into this<br>
> mess with the Apache2 config files, or we would have built the older<br>
> version instead.<br>
<br>
I agree: we need to find the time to move the system to the latest 2.X<br>
series of Apache ... touche ;-)<br>
<br>
> Any insight on where to go next with this would be great.<br>
<br>
Option 1b) followed by httpd-setup.<br>
<br>
Cheers<br>
<br>
Clemens<br>
<br>
--<br>
<br>
***************************************************************<br>
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com<br>
*<br>
* Global Phasing Ltd.<br>
* Sheraton House, Castle Park<br>
* Cambridge CB3 0AX, UK<br>
*--------------------------------------------------------------<br>
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End of sharp-discuss Digest, Vol 41, Issue 2<br>
********************************************<br>
</blockquote></div><br><br clear="all"><br>-- <br>Mark BROOKS<br>Telephone: 0169157968<br>Fax: 0169853715<br>Institut de Biochmie et de Biophysique Moleculaire et Cellulaire<br>UMR8619 - Bât 430 - Université de Paris-Sud<br>
91405 Orsay CEDEX<br>Skype: markabrooks<br>
</div>