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

Francesco Barchetta francesco.barchetta at terradue.com
Fri Dec 18 03:55:34 PST 2015 

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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