[Zoo-discuss] Zoo-project installation and running on Centos-6
Francesco Barchetta
francesco.barchetta at terradue.com
Fri Jan 8 09:20:11 PST 2016
Dear Gerald,
thank you very much for the hint.
I confirm you that this fixes all the runtime errors I had with java also with different jvm versions.
Best regards,
Francesco.
On 08/gen/2016, at 11:30, Fenoy Gerald <gerald.fenoy at geolabs.fr> wrote:
> Dear Francesco,
> let's focus on the java-1.7.0-openjdk case first, can you try to add the following to your main.cfg and confirm that it solves your problem ?
>
> [javax]
> ss=2m
>
>
> Best regards,
>
>
>> Le 7 janv. 2016 à 18:44, Francesco Barchetta <francesco.barchetta at terradue.com> a écrit :
>>
>> Dear Gerald,
>> thanks for updating and validating a new procedure.
>>
>> I’m trying to follow it and the installation phase comes more smooth now.
>>
>> Unfortunately I still cannot run the HelloWorldJava service.
>> This is what I get if I use java-1.7.0-openjdk (and later versions):
>>
>> ./zoo_loader.cgi "Service=WPS&Request=Execute&Version=1.0.0&Identifier=HelloWorldJava&DataInputs=S=myName"
>> Error occurred during initialization of VM
>> java.lang.StackOverflowError
>> at java.lang.Object.<clinit>(Object.java:41)
>>
>> If I use a 1.6.0 version of libjvm.so I get:
>>
>> ./zoo_loader.cgi "Service=WPS&Request=Execute&Version=1.0.0&Identifier=HelloWorldJava&DataInputs=S=myName"
>> <?xml version="1.0" encoding="UTF-8"?>
>> <ows:ExceptionReport xmlns:ows="http://www.opengis.net/ows/1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.opengis.net/ows/1.1 http://schemas.opengis.net/ows/1.1.0/owsExceptionReport.xsd" xml:lang="en-US" version="1.1.0">
>> <ows:Exception exceptionCode="InternalError">
>> <ows:ExceptionText>ZOO Kernel failed to process your request, receiving signal 11 = SIGSEGV</ows:ExceptionText>
>> </ows:Exception>
>> </ows:ExceptionReport>
>>
>> Can you figure out what is the problem here?
>>
>> Thanks in advance,
>>
>> Francesco.
>>
>> On 05/gen/2016, at 08:08, Fenoy Gerald <gerald.fenoy at geolabs.fr> wrote:
>>
>>> 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
>>>>>
>>>>
>>>> _______________________________________________
>>>> 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
>>>
>>
>
>
>
> Gérald Fenoy
> http://wiki.osgeo.org/wiki/User:Djay
>
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