[sharp-discuss] SHARP/autoSHARP installation on Mac OS X 10.5.6

[Clemens Vonrhein]

Dear Masato,

On Fri, Mar 27, 2009 at 02:11:42PM +0000, Masato Akutsu wrote:
> Do you want to start the httpd now ? [y]es/[n]o > y
>
> Error: Apache has not been designed to serve pages while
> running as root. There are known race conditions that
> will allow any local user to read any file on the system.
> If you still desire to serve pages as root then
> add -DBIG_SECURITY_HOLE to the EXTRA_CFLAGS line in your
> src/Configuration file and rebuild the server. It is
> strongly suggested that you instead modify the User
> directive in your httpd.conf file to list a non-root
> user.
>
> ERROR : something went wrong - please see any message above
> and also try running the httpd binary
> /usr/local/xtal/sharp/helpers/darwin/httpd by hand.
> Maybe this binary isn't working on that particular
> platform/operating system? See the file(s)
> /usr/local/xtal/sharp/helpers/*/httpd.README_GPhL.

It seems you're installing SHARP/autoSHARP as root - which is usually
ok for software that doesn't involve something like a httpd. Remember
that all files created by the running httpd (meaning: all
SHARP/autoSHARP output) will then be owned by root. This might not be
ideal.

Furthermore, it seems that on your machine the httpd isn't happy to be
run as 'root' and would need to be compiled differently (with that
-DBIG_SECURITY_HOLE flag ... which has a very telling name).

I would recommend installing our software under a generic 'software'
account (you could name it 'sharp' if you want to use it only for
SHARP/autoSHARP - or 'software', 'xray', 'xtal' or anything else if
you want to use it for all crystallographic software as well).

You could also install our software under your own account if you're
going to be the only peason using it on that particular machine
anyway. Just run the installation in a directory like ~/sharp or such.

If you want to use only the CCP4i autoSHARP interface (the one that
comes with the latest CCP4 6.1.1 - but see the 'problems' page on
www.ccp4.ac.uk for updated files!): no running httpd is needed anyway
and you could just skip that step. However, the CCP4i interface to
autoSHARP has significantly less functionality: all those well and
tightly integrated tools for analysis of residual maps, density
modification and fine-tuning SHARP aren't in there. It will runn the
same autoSHARP steps though ...

Cheers

Clemens

>
>
> NOTE : unable to start httpd on this port - try next one
>
> Continue [y]es/[n]o/[e]xit/[s]kip >
>> ***************************************************************
>
>
> I am afraid I do not know how to run this by hand.
> Do I need to do something with
> /usr/local/xtal/sharp/helpers/darwin/httpd.README_GPhL ?
>
> Best regards,
> Masato
>
>
> On 27 Mar 2009, at 08:07, Clemens Vonrhein wrote:
>
>> Dear Masato,
>>
>> On Fri, Mar 27, 2009 at 01:10:23AM +0000, Masato Akutsu wrote:
>>> However, I got another WARNING message at the section of server  
>>> setup as
>>> below.
>>> 4. list of directories for
>>>     LD_LIBRARY_PATH/DYLD_LIBRARY_PATH variable :
>>>     [/usr/local/ccp4-6.1.1/share/XIAROOT/xia2//binaries/mac_386:] >
>>> WARNING : invalid answer - try again.
>>
>> Yes, that installation part is maybe a bit picky: it basically tests
>> that each directory in that DYLD_LIBRARY_PATH variable (picked up rom
>> your environment) exists. So there are two possible explanations:
>>
>>  a) the directory
>>  /usr/local/ccp4-6.1.1/share/XIAROOT/xia2//binaries/mac_386 doesnt
>>  exist
>>
>>  b) it is confused by that extra ':' at the end
>>
>>> I would be most grateful if anyone could give me a hint.
>>
>> Ideally, try fixing your DYLD_LIBRARY_PATH settings before running
>> 'installSHARP -F'. I'm not sure where this is set (maybe in one of the
>> CCP4 setup scripts?) though.
>>
>> Or when you get stuck at that point, give it a valid entry like
>>
>>  /usr/local/ccp4-6.1.1/share/XIAROOT/xia2/binaries/mac_386
>>
>> (i.e. without the trailing ':').
>>
>> Cheers
>>
>> Clemens
>>
>> -- 
>>
>> ***************************************************************
>> * Clemens Vonrhein, Ph.D.     vonrhein AT GlobalPhasing DOT com
>> *
>> *  Global Phasing Ltd.
>> *  Sheraton House, Castle Park
>> *  Cambridge CB3 0AX, UK
>> *--------------------------------------------------------------
>> * BUSTER Development Group      (http://www.globalphasing.com)
>> ***************************************************************
>

-- 

***************************************************************
* Clemens Vonrhein, Ph.D.     vonrhein AT GlobalPhasing DOT com
*
*  Global Phasing Ltd.
*  Sheraton House, Castle Park 
*  Cambridge CB3 0AX, UK
*--------------------------------------------------------------
* BUSTER Development Group      (http://www.globalphasing.com)
***************************************************************