[Zoo-discuss] Zoo-project installation and running on Centos-6

Fenoy Gerald gerald.fenoy at geolabs.fr
Tue Jan 5 00:08:40 PST 2016 

Dear Francesco,
I do apologize for answering so late.

After you send this email, I’ve setup a fresh CentOS 6 and used the following setup procedure :

  rpm -Uvh http://elgis.argeo.org/repos/6/elgis-release-6-6_0.noarch.rpm
  rpm -Uvh \
    http://download.fedoraproject.org/pub/epel/6/x86_64/epel-release-6-8.noarch.rpm
  wget\
    http://proj.badc.rl.ac.uk/cedaservices/raw-attachment/ticket/670/armadillo-3.800.2-1.el6.x86_64.rpm
  yum install armadillo-3.800.2-1.el6.x86_64.rpm
  yum install hdf5.so.6
  yum install gcc-c++ zlib-devel libxml2-devel bison openssl \
    python-devel subversion libxslt-devel libcurl-devel \
    gdal-devel proj-devel libuuid-devel openssl-devel fcgi-devel
  yum install java-1.7.0-openjdk-devel

Then I make sure tu use correct version of both java and java using the update-alternatives --config java and update-alternatives --config java commands

Everything now works well for the Java support on this platform. There were few mistakes which was fixed on the way inside the ZOO-Project Java support which did not appear when using this support on MacOS X.

I have jus updated the installation documentation for CentOS and I thank you for your comment and your help for this.

Best regards,

> Le 18 déc. 2015 à 18:55, Francesco Barchetta <francesco.barchetta at terradue.com> a écrit :
> 
> Dear Gerald,
> 
> thank you for the quick response.
> 
>> For the parameters you added to your httpd.conf for LD_LIBRARY_PATH, I think it is not required. Nevertheless, you should need to run ldconfig after you setup your ZOO-Kernel (by running make install). This should probably solve your issue with GetCapabilities and DescribeProcess.
> 
> as you can see from the procedure I’ve described, I did the make install but it wasn’t enough.
> 
>> For the issue when trying to Execute a Java service, I supposed that the issue came because you did not setup the ZOO-API Java Class. 
> 
> Sorry to have missed this in the previous email. I’ve compiled and copied the ZOO-API Java Class but nothing has changed. This is the content of my cgi environment:
> 
> -rw-r--r-- 1 root root   1527 Dec 17 16:30 HelloJava.class
> -rwxr-xr-x 1 root root    691 Dec 18 12:43 HelloWorldJava.zcfg
> -rwxr-xr-x 1 root root  48038 Dec 17 15:29 libZOO.so
> -rw-r--r-- 1 root root    759 Dec 17 16:05 main.cfg
> -rw-r--r-- 1 root root   1580 Dec 17 16:35 test_service.py
> -rw-r--r-- 1 root root    840 Dec 17 16:43 test_service.pyc
> -rw-r--r-- 1 root root    648 Dec 17 15:29 ZOO.class
> -rwxr-xr-x 1 root root 445354 Dec 17 16:05 zoo_loader.cgi
> 
>> Maybe it can help me if you can provide the back trace from gdb after the segfault.
> 
> Here is the complete backtrace:
> 
> (gdb) run "Service=WPS&request=Execute&service=WPS&version=1.0.0&Identifier=HelloWorldJava&DataInputs=S=Test"
> Starting program: /var/www/cgi-bin/zoo_loader.cgi "Service=WPS&request=Execute&service=WPS&version=1.0.0&Identifier=HelloWorldJava&DataInputs=S=Test"
> [Thread debugging using libthread_db enabled]
> [New Thread 0x7fffe7283700 (LWP 7268)]
> [New Thread 0x7fffe7182700 (LWP 7269)]
> [New Thread 0x7fffe6b8b700 (LWP 7270)]
> 
> Program received signal SIGSEGV, Segmentation fault.
> 0x00007ffff500204a in frame::frame(long*, long*) () from /usr/java/jdk1.6.0_35/jre/lib/amd64/server/libjvm.so
> Missing separate debuginfos, use: debuginfo-install libidn-1.18-2.el6.x86_64
> (gdb) bt
> #0  0x00007ffff500204a in frame::frame(long*, long*) () from /usr/java/jdk1.6.0_35/jre/lib/amd64/server/libjvm.so
> #1  0x00007ffff51d6acf in java_lang_Throwable::fill_in_stack_trace(Handle, Thread*) () from /usr/java/jdk1.6.0_35/jre/lib/amd64/server/libjvm.so
> #2  0x00007ffff51d6b79 in java_lang_Throwable::fill_in_stack_trace(Handle) () from /usr/java/jdk1.6.0_35/jre/lib/amd64/server/libjvm.so
> #3  0x00007ffff5126d67 in Exceptions::throw_stack_overflow_exception(Thread*, char const*, int) () from /usr/java/jdk1.6.0_35/jre/lib/amd64/server/libjvm.so
> #4  0x00007ffff51d04e1 in JavaCalls::call_helper(JavaValue*, methodHandle*, JavaCallArguments*, Thread*) ()
>   from /usr/java/jdk1.6.0_35/jre/lib/amd64/server/libjvm.so
> #5  0x00007ffff5400869 in os::os_exception_wrapper(void (*)(JavaValue*, methodHandle*, JavaCallArguments*, Thread*), JavaValue*, methodHandle*, JavaCallArguments*, Thread*) () from /usr/java/jdk1.6.0_35/jre/lib/amd64/server/libjvm.so
> #6  0x00007ffff51d03b5 in JavaCalls::call(JavaValue*, methodHandle, JavaCallArguments*, Thread*) () from /usr/java/jdk1.6.0_35/jre/lib/amd64/server/libjvm.so
> #7  0x00007ffff519ffb5 in instanceKlass::call_class_initializer_impl(instanceKlassHandle, Thread*) ()
>   from /usr/java/jdk1.6.0_35/jre/lib/amd64/server/libjvm.so
> #8  0x00007ffff519e538 in instanceKlass::initialize_impl(instanceKlassHandle, Thread*) () from /usr/java/jdk1.6.0_35/jre/lib/amd64/server/libjvm.so
> #9  0x00007ffff519d8fa in instanceKlass::initialize(Thread*) () from /usr/java/jdk1.6.0_35/jre/lib/amd64/server/libjvm.so
> #10 0x00007ffff519e7fc in instanceKlass::initialize_impl(instanceKlassHandle, Thread*) () from /usr/java/jdk1.6.0_35/jre/lib/amd64/server/libjvm.so
> #11 0x00007ffff519d8fa in instanceKlass::initialize(Thread*) () from /usr/java/jdk1.6.0_35/jre/lib/amd64/server/libjvm.so
> #12 0x00007ffff550f654 in Threads::create_vm(JavaVMInitArgs*, bool*) () from /usr/java/jdk1.6.0_35/jre/lib/amd64/server/libjvm.so
> #13 0x00007ffff520b790 in JNI_CreateJavaVM () from /usr/java/jdk1.6.0_35/jre/lib/amd64/server/libjvm.so
> #14 0x000000000040ceb4 in zoo_java_support ()
> #15 0x0000000000406fa3 in loadServiceAndRun (myMap=0x7fffffffe188, s1=0x65d0b0, request_inputs=0x65be20, inputs=<value optimized out>, ioutputs=
>    0x7fffffffe178, eres=0x7fffffffe19c) at zoo_service_loader.c:622
> #16 0x00000000004090c6 in runRequest (inputs=<value optimized out>) at zoo_service_loader.c:2141
> #17 0x000000000040628a in cgiMain () at zoo_loader.c:402
> #18 0x000000000042b63f in main (argc=2, argv=0x7fffffffe458) at cgic.c:312
> 
> 
> Best regards,
> 
> Francesco.
> 
> On 18/dic/2015, at 11:32, Fenoy Gerald <gerald.fenoy at geolabs.fr> wrote:
> 
>> Hello Francesco,
>> nice to hear that you are willing to adopt the ZOO-Project.
>> 
>> First of all, I have to say that this documentation has been written 5 years ago, so any help on setting up the ZOO-Project on CentOS is probably needed. The original version was there : [1].
>> 
>> For the package names I have to admit that I don’t have access to any CentOS host to verify the package names, so the correct names will help us to fix this part of the documentation.
>> 
>> For the parameters you added to your httpd.conf for LD_LIBRARY_PATH, I think it is not required. Nevertheless, you should need to run ldconfig after you setup your ZOO-Kernel (by running make install). This should probably solve your issue with GetCapabilities and DescribeProcess.
>> 
>> I suppose that there is no need anymore for removing any line from ulinet.c to get it working. I hope you can confirm this by executing services passing parameter by reference rather than by value.
>> 
>> For the issue when trying to Execute a Java service, I supposed that the issue came because you did not setup the ZOO-API Java Class. So I tried it locally but I have a standard Exception report returned in this case and it contains the following information: * Exception in thread "main" java.lang.NoClassDefFoundError: ZOO * . So there should be no problem here. Maybe it can help me if you can provide the back trace from gdb after the segfault.
>> 
>> I hope to hear back from you,
>> Best regards,
>> 
>> [1] http://zoo-project.org/trac/wiki/ZooDocumentation/ZOOKernel/CentOS_installation 
>> 
>> 
>>> Le 18 déc. 2015 à 10:47, Francesco Barchetta <francesco.barchetta at terradue.com> a écrit :
>>> 
>>> Hello!
>>> 
>>> In the context of our Earth Observation projects my company (Terradue UK) would like to adopt your implementation of WPS, .
>>> 
>>> The typical environment where to install the server is a VM with CentOS release 6.7 x86_64 .
>>> 
>>> INSTALLATION:
>>> 
>>> From the official documentation:
>>> 
>>> http://zoo-project.org/docs/install/centos.html
>>> 
>>> If I've tried to follow the list of commands I quickly found some issue or incorrect steps:
>>> 
>>> yum install apache2
>>> do you mean httpd?
>>> yum install build-essentials
>>> do you mean yum groupinstall "Development Tools” ?
>>> yum install gcc-c++ 
>>> yum install libxml2-devel 
>>> yum install zlib-devel 
>>> yum install bison 
>>> yum install openssl   
>>> yum install python-devel
>>> yum install subversion 
>>> 
>>> Additional prerequisites found:
>>> 
>>> yum install libxslt-devel.x86_64 
>>> yum install libcurl-devel 
>>> yum install gdal-devel 
>>> yum install proj-devel.x86_64 
>>> yum install libuuid-devel
>>> yum install openssl-devel
>>> 
>>> FOR GDAL 1.8.0 (otherwise zoo-kernel will complain about VSILFILE)
>>> 
>>> wget http://download.osgeo.org/gdal/gdal-1.8.0.tar.gz
>>> tar xzf gdal-1.8.0.tar.gz
>>> cd gdal-1.8.0
>>> ./configure  # add your options here
>>> make
>>> make install
>>> 
>>> TO INSTALL FASTCGI
>>> 
>>> wget http://www.fastcgi.com/dist/fcgi.tar.gz
>>> tar xzf fcgi.tar.gz
>>> cd fcgi-2.4.1-SNAP-0311112127/	
>>> 
>>> PATCH (from http://stackoverflow.com/questions/4577453/fcgio-cpp50-error-eof-was-not-declared-in-this-scope):
>>> 
>>> 	--- include/fcgio.h 2012-01-23 15:23:51.136063795 +0000
>>> 	+++ include/fcgio.h 2012-01-23 15:22:19.057221383 +0000
>>> 	@@ -31,6 +31,7 @@
>>> 	#define FCGIO_H
>>> 
>>> 	 #include <iostream>
>>> 	+#include <stdio.h>
>>> 
>>> 	 #include "fcgiapp.h"
>>> 
>>> ./configure
>>> make
>>> make install
>>> echo /usr/local/lib >> /etc/ld.so.conf.d/local.conf
>>> ldconfig
>>> 
>>> TO INSTALL autoconf tools (OK)
>>> 
>>> TO INSTALL FLEX TOOL (OK)
>>> 
>>> CURL:
>>> 
>>> To avoid the installation of a different version of Curl, I want to follow the guide about changing the file ulinet.c but the link to the code is broken and:
>>> 
>>> line 173 is :
>>> 
>>> printf("\n**[PROXY SETTINGS DETECTION %s (%d) %s:%li (%s)]**\n",proto,proxy_enabled,(char*)proxy_host,proxy_port,buffer);
>>> 
>>> line 175 is a white line
>>> 
>>> Should I comment these lines?
>>> 
>>> Anyway our base line version is 7.19.7. Is it good?
>>> 
>>> INSTALL ZOO-KERNEL 
>>> Since this section is totally missing I got inspiration from the previous version (still incomplete and not working):
>>> 
>>> http://www.zoo-project.org/docs/kernel/install-centos.html
>>> 
>>> svn co http://svn.zoo-project.org/svn/trunk zoo-project
>>> cd zoo-project/thirds/cgic206
>>> edit file Makefile in order to set the current fgci path adding:
>>> 	LIBS= -L./ -lcgic /usr/local/lib/libfcgi.so
>>> make 
>>> cd ../../zoo-project/zoo-kernel
>>> autoconf
>>> ./configure --with-java=/usr/java/jdk1.6.0_35/ --with-python --with-gdal_config=/usr/bin/gdal-config
>>> make zoo_loader.cgi
>>> make install
>>> cp main.cfg /var/www/cgi-bin/
>>> cp zoo_loader.cgi /var/www/cgi-bin/
>>> 
>>> In httpd.conf I have to add:
>>> SetEnv LD_LIBRARY_PATH /usr/local/lib/
>>> 
>>> Now the GetCapabilities and DescribeProcess calls work fine.
>>> 
>>> EXECUTE:
>>> 
>>> HelloPy works fine.
>>> 
>>> HelloWorldJava is not working:
>>> 
>>> From the Browser => 500 Internal Server Error
>>> 
>>> Form the command line:
>>> 
>>> ./zoo_loader.cgi "Service=WPS&request=Execute&service=WPS&version=1.0.0&Identifier=HelloWorldJava&DataInputs=S=Test"Content-Type: text/xml; charset=UTF-8
>>> Status: 501 Internal Server Error
>>> 
>>> Segmentation fault
>>> 
>>> 
>>> With gdb:
>>> 
>>> (gdb) run "Service=WPS&request=Execute&service=WPS&version=1.0.0&Identifier=HelloWorldJava&DataInputs=S=Test"
>>> Starting program: /var/www/cgi-bin/zoo_loader.cgi "Service=WPS&request=Execute&service=WPS&version=1.0.0&Identifier=HelloWorldJava&DataInputs=S=Test"
>>> [Thread debugging using libthread_db enabled]
>>> [New Thread 0x7fffe7283700 (LWP 29445)]
>>> [New Thread 0x7fffe7182700 (LWP 29446)]
>>> [New Thread 0x7fffe6b8b700 (LWP 29447)]
>>> 
>>> Program received signal SIGSEGV, Segmentation fault.
>>> 0x00007ffff500204a in frame::frame(long*, long*) () from /usr/java/jdk1.6.0_35/jre/lib/amd64/server/libjvm.so
>>> 
>>> 
>>> CONCLUSIONS
>>> 
>>> I hope that my experience could help you to improve the installation procedure description and I hope you could help me to find out the reason of the failed execution.
>>> 
>>> Best Regards,
>>> 
>>> Francesco Barchetta
>>> 
>>> Terradue UK
>>> _______________________________________________
>>> Zoo-discuss mailing list
>>> Zoo-discuss at lists.osgeo.org
>>> http://lists.osgeo.org/mailman/listinfo/zoo-discuss
>> 
>> 
>> 
>> Gérald Fenoy
>> http://wiki.osgeo.org/wiki/User:Djay
>> 
> 
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Gérald Fenoy
http://wiki.osgeo.org/wiki/User:Djay

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