Mark,
The paths in /areaDetector-2-1/configure/CONFIG_SITE.local are configured
according to the instructions. But I realized that this file may actually
not get included in the /areaDetector-2-1/ADCore/ADApp/nexusSrc/Makefile,
hence the errors that appear when building the source code in
/opt/epics/areaDetector-2-1/ADCore/ADApp/nexusSrc. (I remember now that
there was another error related to inclusion of hdf5.h, which I'd initially
solved by copying the file)
If I edit /areaDetector-2-1/ADCore/ADApp/nexusSrc/Makefile and replace the
macros HDF5_INCLUDE, HDF5_LIB and SZIP_LIB with the actual values, then
those errors (reported in the previous emails) no longer appear, but I end
up in another error (see attached file err3.txt)
So the questions now are:
Q1: Could there be an 'include' problem in
/areaDetector-2-1/ADCore/ADApp/nexusSrc/Makefile, since the values of the 3
macros above do not get propagated to the compiler?
Q2: are there any restrictions related to the placement of areaDetector-x-y
top folder relative the epics base or synApps folder? Should I place
areaDetector-2-1 inside synApps_5_7/support/?
Q3: are there any compatibility issues between areaDetector-2-1 and
synApps_5_7? I'm asking this because in
/areaDetector-2-1/configure/EXAMPLE_RELEASE_PRODS.local the default versions
for some modules are newer than the ones found in synApps_5_7 (which is the
most recent release to this date).
Thanks again
Cristi
-----Original Message-----
From: Mark Rivers [mailto:[email protected]]
Sent: Monday, March 9, 2015 2:15 PM
To: Cristian Savlovschi; [email protected]
Subject: RE: Problem with libhdf5.a when installling areaDetector-2-1
Hi Christi,
> A similar message was reported also for libsz.a, so I made a symbolic link
for the 2 libs, hoping to overcome this error:
> ln -s /usr/local/hdf5/lib/libhdf5.a
/opt/epics/areaDetector-2-1/ADCore/ADApp/nexusSrc/O.linux-x86_64
> ln -s /usr/local/lib/libhsz.a
/opt/epics/areaDetector-2-1/ADCore/ADApp/nexusSrc/O.linux-x86_64
You should not make those links. Rather you should follow the instructions
in the installation guide for areaDetector 2-X here:
https://github.com/areaDetector/areaDetector/blob/master/INSTALL_GUIDE.md
Edit the top-level areaDetector-2-1/configure/CONFIG_SITE.local (start with
EXAMPLE_CONFIG_SITE.local as an example) to define where the HDF5, SZLIB,
etc. libraries are.
Mark
________________________________
From: Cristian Savlovschi [[email protected]]
Sent: Monday, March 09, 2015 3:43 AM
To: Mark Rivers; [email protected]
Subject: RE: Problem with libhdf5.a when installling areaDetector-2-1
Hi Mark,
Thanks for the quick reply,
Here are some more details about my build process that will help explain
this error message:
1. My EPICS directory tree looks like this:
/opt/epics/
/areaDetector-2-1
/......
/base-3.14.12.4
/IOC_example1
/synApps_5_7
/support
/allenBradley-2-2
/areaDetector-1-9-1
/asyn-4-21
/.....
2. I did install hdf5 in /usr/local/hdf5 (although reported a lot of
warnings during the build - type conversions etc ); the libhdf5.a is located
in /usr/local/hdf5/lib. In this configuration the 'make' of areaDetector
fails with:
...
make -C ./nexusSrc install
make[3]: Entering directory
`/opt/epics/areaDetector-2-1/ADCore/ADApp/nexusSrc'
make -C O.linux-x86_64 -f ../Makefile TOP=../../.. T_A=linux-x86_64 install
make[4]: Entering directory
`/opt/epics/areaDetector-2-1/ADCore/ADApp/nexusSrc/O.linux-x86_64'
make[4]: *** No rule to make target `../../../lib/linux-x86_64/libhdf5.a',
needed by `libNeXus.so'. Stop.
make[4]: Leaving directory
`/opt/epics/areaDetector-2-1/ADCore/ADApp/nexusSrc/O.linux-x86_64'
make[3]: *** [install.linux-x86_64] Error 2
A similar message was reported also for libsz.a, so I made a symbolic
link for the 2 libs, hoping to overcome this error:
ln -s /usr/local/hdf5/lib/libhdf5.a
/opt/epics/areaDetector-2-1/ADCore/ADApp/nexusSrc/O.linux-x86_64
ln -s /usr/local/lib/libhsz.a
/opt/epics/areaDetector-2-1/ADCore/ADApp/nexusSrc/O.linux-x86_64
3. Not sure if this is relevant, but in an earlier stage of the areaDetector
make, I had received another error mentioning that there was a duplicate of
AREA_DETECTOR macro (found in both
/opt/epics/areaDetector-2-1/configure/RELEASE_PATHS.local and
/opt/epics/synApps_5_7 /support/areaDetector-1-9-1/RELEASE),
so I commented out the latter.
regs,
Cristi
-----Original Message-----
From: Mark Rivers [mailto:[email protected]]
Sent: Friday, March 6, 2015 6:37 PM
To: Cristian Savlovschi; [email protected]
Subject: RE: Problem with libhdf5.a when installling areaDetector-2-1
Hi Cristi,
I don't understand this error message:
/usr/bin/ld: /opt/epics/areaDetector-2-1/ADCore/lib/linux-x86_64/libhdf5.a
There should not be a libhdf5.a in that directory. libhdf5 should be in
some directory outside of ADCore. It looks like in your case you are
building hdf5 in /usr/local/hdf5. Where did that file in
ADCore/lib/linux-x86_64 come from?
Here is the contents of the ADCore/lib/linux-x86_64/ directory on my system
after a successful build of ADCore.
/home/epics/devel/areaDetector/ADCore/lib/linux-x86_64
corvette:ADCore/lib/linux-x86_64>ls -l
total 15728
-r--r--r-- 1 epics epics 1649396 Mar 5 15:36 libADBase.a -r-xr-xr-x 1 epics
epics 727178 Mar 5 15:36 libADBase.so
-r--r--r-- 1 epics epics 5930442 Mar 6 09:57 libNDPlugin.a -r-xr-xr-x 1
epics epics 2518160 Mar 6 09:57 libNDPlugin.so
-r--r--r-- 1 epics epics 483936 Mar 5 15:36 libNeXus.a -r-xr-xr-x 1 epics
epics 262674 Mar 5 15:36 libNeXus.so
-r--r--r-- 1 epics epics 2299174 Mar 5 15:36 libnetCDF.a -r-xr-xr-x 1 epics
epics 1645681 Mar 5 15:36 libnetCDF.so
-r--r--r-- 1 epics epics 373970 Mar 5 15:40 libsimDetector.a -r-xr-xr-x 1
epics epics 194233 Mar 5 15:40 libsimDetector.so
Mark
________________________________
From: [email protected]<mailto:[email protected]>
[[email protected]] on behalf of Cristian Savlovschi
[[email protected]]
Sent: Friday, March 06, 2015 6:44 AM
To: [email protected]<mailto:[email protected]>
Subject: Problem with libhdf5.a when installling areaDetector-2-1
Hi,
I'm trying to create a demo project based on EPICS, in the following
configuration:
IOC (CA server) running on UBUNTU 14.04 linux-x86_64 CA Client (CSS) running
on Windows 8 I've installed EPICS Base 3.14.12.4 + synApps 5.7 succesfully
and was able to run the IOC for DG645 delay generator and connect to the hw
device.
Now I'm stuck on the next step, which is to install another IOC application,
for a Point Grey Flea3 CCD camera.
The driver for this device has been added to areaDetector package starting
with release 2.0 (Apr 2014). The most recent version of areaDetector in
synApps (at present time - March 2015) is 1.9.1, therefore I've decided to
update this package. I've downloaded it from github and tried to install it
in a separate 'TOP' folder following the installation instructions in
https://github.com/areaDetector/areaDetector/blob/master/INSTALL_GUIDE.md
After customizing all the configuration files and installing all 3rd party
packages, my 'make' is failing with the following error message:
make[4]: Entering directory
`/opt/epics/areaDetector-2-1/ADCore/ADApp/nexusSrc/O.linux-x86_64'
/usr/bin/g++ -o libNeXus.so -shared -fPIC -Wl,-hlibNeXus.so
-L/opt/epics/areaDetector-2-1/ADCore/lib/linux-x86_64
-Wl,-rpath,/opt/epics/areaDetector-2-1/ADCore/lib/linux-x86_64 -m64
napi.o napi5.o napiu.o nxdataset.o nxio.o nxstack.o nxxml.o stptok.o
-lhdf5 -lsz -lpthread -lreadline -lm -lrt -ldl -lgcc
/usr/bin/ld:
/opt/epics/areaDetector-2-1/ADCore/lib/linux-x86_64/libhdf5.a(H5.o):
relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making
a shared object; recompile with -fPIC
/opt/epics/areaDetector-2-1/ADCore/lib/linux-x86_64/libhdf5.a:
error adding symbols: Bad value
collect2: error: ld returned 1 exit status
I cannot get pass this point, even after trying to rebuild the HDF5 package
with additional -fPIC flag:
LDFLAGS=-fPIC ./configure --prefix=/usr/local/hdf5 --with-szlib=/usr/local
Any suggestions?
Note that I'm a EPICS & Linux beginner (~1 month)..
Thanks!
Cristi S
make -C ./pluginSrc install
make[3]: Entering directory `/opt/epics/areaDetector-2-1/ADCore/ADApp/pluginSrc'
perl /opt/epics/base-3.14.12.4/bin/linux-x86_64/makeMakefile.pl O.linux-x86_64 ../../..
mkdir O.Common
make -C O.linux-x86_64 -f ../Makefile TOP=../../.. T_A=linux-x86_64 install
make[4]: Entering directory `/opt/epics/areaDetector-2-1/ADCore/ADApp/pluginSrc/O.linux-x86_64'
Installing dbd file ../../../dbd/NDPluginSupport.dbd
Installing dbd file ../../../dbd/NDFileJPEG.dbd
Installing dbd file ../../../dbd/NDFileMagick.dbd
Installing dbd file ../../../dbd/NDFileNetCDF.dbd
Installing dbd file ../../../dbd/NDFileNexus.dbd
Installing dbd file ../../../dbd/NDFileHDF5.dbd
Installing dbd file ../../../dbd/NDFileTIFF.dbd
Installing dbd file ../../../dbd/NDFileNull.dbd
Installing dbd file ../../../dbd/NDPluginColorConvert.dbd
Installing dbd file ../../../dbd/NDPluginOverlay.dbd
Installing dbd file ../../../dbd/NDPluginProcess.dbd
Installing dbd file ../../../dbd/NDPluginROI.dbd
Installing dbd file ../../../dbd/NDPluginROIStat.dbd
Installing dbd file ../../../dbd/NDPluginStats.dbd
Installing dbd file ../../../dbd/NDPluginStdArrays.dbd
Installing dbd file ../../../dbd/NDPluginTransform.dbd
Installing dbd file ../../../dbd/NDPluginAttribute.dbd
Installing dbd file ../../../dbd/NDPluginCircularBuff.dbd
Installing generic include file ../../../include/NDFileHDF5.h
Installing generic include file ../../../include/NDFileHDF5Dataset.h
Installing generic include file ../../../include/NDFileHDF5Layout.h
Installing generic include file ../../../include/NDFileHDF5LayoutXML.h
Installing generic include file ../../../include/NDFileJPEG.h
Installing generic include file ../../../include/NDFileMagick.h
Installing generic include file ../../../include/NDFileNetCDF.h
Installing generic include file ../../../include/NDFileNexus.h
Installing generic include file ../../../include/NDFileNull.h
Installing generic include file ../../../include/NDFileTIFF.h
Installing generic include file ../../../include/NDPluginAttribute.h
Installing generic include file ../../../include/NDPluginColorConvert.h
Installing generic include file ../../../include/NDPluginDriver.h
Installing generic include file ../../../include/NDPluginFile.h
Installing generic include file ../../../include/NDPluginOverlay.h
Installing generic include file ../../../include/NDPluginOverlayTextFont.h
Installing generic include file ../../../include/NDPluginProcess.h
Installing generic include file ../../../include/NDPluginROI.h
Installing generic include file ../../../include/NDPluginROIStat.h
Installing generic include file ../../../include/NDPluginStats.h
Installing generic include file ../../../include/NDPluginStdArrays.h
Installing generic include file ../../../include/NDPluginTransform.h
Installing generic include file ../../../include/NDPluginCircularBuff.h
Installing generic include file ../../../include/NDArrayRing.h
/usr/bin/g++ -c -D_POSIX_C_SOURCE=199506L -D_POSIX_THREADS -D_XOPEN_SOURCE=500 -D_X86_64_ -DUNIX -D_BSD_SOURCE -Dlinux -D_REENTRANT -O3 -g -Wall -m64 -fPIC -MMD -I. -I../O.Common -I. -I.. -I../../../include/os/Linux -I../../../include -I/opt/epics/base-3.14.12.4/include/os/Linux -I/opt/epics/base-3.14.12.4/include -I/opt/epics/synApps_5_7/support/asyn-4-21/include ../NDPluginDriver.cpp
../NDPluginDriver.cpp: In member function â??virtual void NDPluginDriver::processCallbacks(NDArray*)â??:
../NDPluginDriver.cpp:60:34: error: â??setTimeStampâ?? was not declared in this scope
setTimeStamp(&pArray->epicsTS);
^
make[4]: *** [NDPluginDriver.o] Error 1
make[4]: Leaving directory `/opt/epics/areaDetector-2-1/ADCore/ADApp/pluginSrc/O.linux-x86_64'
- Replies:
- RE: Problem with libhdf5.a when installling areaDetector-2-1 Mark Rivers
- RE: Problem with libhdf5.a when installling areaDetector-2-1 Mark Rivers
- References:
- Problem with libhdf5.a when installling areaDetector-2-1 Cristian Savlovschi
- RE: Problem with libhdf5.a when installling areaDetector-2-1 Mark Rivers
- RE: Problem with libhdf5.a when installling areaDetector-2-1 Cristian Savlovschi
- RE: Problem with libhdf5.a when installling areaDetector-2-1 Mark Rivers
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