Skip to content

Evio 6 dev tmp #37

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
jonzarling merged 14 commits into from
Sep 10, 2025
Merged

Evio 6 dev tmp #37

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
14 commits
Select commit Hold shift + click to select a range
3d6df89
Add install to README instructions (cmake C++ build). Add new utiliti…
jonzarling Jul 25, 2025
b7be09c
Add actual code for merging program. Work on small test files at least.
jonzarling Jul 25, 2025
ce97724
Add java util for merging files, apparently more robust than analogou…
jonzarling Jul 30, 2025
a931884
Move links to top of readme again
jonzarling Jul 31, 2025
21da8a5
More readme cleanup
jonzarling Jul 31, 2025
a8d75ec
Java: ensure header recovery check has enough to do lookback. Separat…
jonzarling Aug 8, 2025
0edfe78
Cmake cleanup, add proper install target, plus update github actions
jonzarling Aug 8, 2025
5d05036
Update main README, add new ones for explaining folder contents
jonzarling Aug 8, 2025
d49b564
Don't quit if one encounters empty BANK/SEGMENT/TAGSEGMENT, just igno…
jonzarling Aug 8, 2025
53480ce
C++ program that prints evio contents (initial version)
jonzarling Aug 8, 2025
d4413b6
Rename and fix output filename
jonzarling Aug 8, 2025
eb460fd
Fix merge program to support V6 files (without compression in output)
jonzarling Aug 11, 2025
baa719f
BIG memory leak fix. Put bytes into vector instead of array.
jonzarling Aug 11, 2025
04fe2ea
Remove unfinished utility program before merging into main (but only …
jonzarling Sep 10, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion .github/workflows/c_tests.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@ jobs:
run: cmake -S . -B build -DMAKE_EXAMPLES=1

- name: Build
run: cmake --build build -- -j$(nproc)
run: cmake --build build --target install --parallel

- name: Run tests
working-directory: build
Expand Down
3 changes: 3 additions & 0 deletions .gitignore
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,7 @@ build/
jbuild/
lib/
bin/
tmp/
doxyerrors.log
target/
doc/javadoc
Expand All @@ -37,3 +38,5 @@ doc/doxygen/C
doc/source/
config.log

# Ignore typical install directory type
Linux-*/
49 changes: 38 additions & 11 deletions CMakeLists.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,22 +1,26 @@
# See instructions in README.md for building and installing

### VERSION DEFINITIONS ###
cmake_minimum_required(VERSION 3.22)
project(evio VERSION 6.1.0 LANGUAGES C CXX)

# C/C++ standard and build options
set(CMAKE_C_STANDARD 11)
set(CMAKE_C_STANDARD_REQUIRED ON)
set(CMAKE_CXX_STANDARD 20)
# C/C++ build options
set(CMAKE_C_STANDARD_REQUIRED ON)
set(CMAKE_CXX_STANDARD_REQUIRED ON)
set(CMAKE_DEBUG_POSTFIX -dbg)
add_compile_options(-Wall)
add_compile_options(-Wall) # Enable all warnings

# Build options (and defaults)
# Includes
include(GNUInstallDirs)
include(FindPackageHandleStandardArgs) # find_package_handle_standard_args()
include(CTest)

# Build option parameters (and defaults)
option(C_ONLY "SKIP building C++ library, build C only" OFF)
option(MAKE_EXAMPLES "Build example/test programs" OFF)
option(USE_FILESYSTEMLIB "Use C++ <filesystem> instead of Boost" OFF)
option(DISRUPTOR_FETCH "Allow CMake to download Disruptor if not found" ON)
include(GNUInstallDirs)
include(FindPackageHandleStandardArgs) # find_package_handle_standard_args()
include(CTest)

# Add custom find_package for Disruptor
list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake/modules")
Expand Down Expand Up @@ -51,7 +55,10 @@ elseif (DEFINED ENV{CODA})
else()
# Use default CMAKE_INSTALL_PREFIX
set(INSTALL_DIR_DEFINED 1)
set(CMAKE_INSTALL_PREFIX ${CMAKE_CURRENT_SOURCE_DIR}/${ARCH})
set(CMAKE_INSTALL_INCLUDEDIR ${CMAKE_INSTALL_PREFIX}/include)
message(STATUS "Installing to default location: ${CMAKE_INSTALL_PREFIX}")
message(STATUS "Installing includes to default location: ${CMAKE_INSTALL_INCLUDEDIR}")
endif()

# Boost libs
Expand Down Expand Up @@ -98,12 +105,13 @@ file(GLOB C_LIB_FILES "src/libsrc/*.c")
# C++ source files
file(GLOB CPP_LIB_FILES "src/libsrc++/*.cpp")
file(GLOB CPP_HEADER_FILES "src/libsrc++/*.h")
# A few extras required
# C++ utility files
file(GLOB CPP_UTILS_FILES "src/utils/cpp/*.cpp")
# A few extras required for examples
if(MAKE_EXAMPLES)
list(APPEND CPP_HEADER_FILES src/test/cpp/EvioTestHelper.h)
file(GLOB TEST "src/test/cpp/*.cpp")
file(GLOB TESTC "src/test/c/*.c")
list(APPEND CPP_HEADER_FILES src/test/cpp/EvioTestHelper.h)
# list(APPEND CPP_LIB_FILES src/test/cpp/EvioTestHelper.h)
endif()

# BUILD C++ LIBRARY (unless otherwise specified)
Expand Down Expand Up @@ -142,6 +150,25 @@ if(NOT C_ONLY)
${DISRUPTOR_INCLUDE_DIR}
)

# Build utility programs
foreach(fileName ${CPP_UTILS_FILES})
# Get file name with no directory or extension as executable name
get_filename_component(execName ${fileName} NAME_WE)
# Create executable from file
add_executable(${execName} ${fileName})
# Put debug extension on if applicable
set_target_properties(${execName} PROPERTIES DEBUG_POSTFIX ${CMAKE_DEBUG_POSTFIX})
# Needs these libs
target_link_libraries(${execName} eviocc pthread ${Boost_LIBRARIES} ${LZ4_LIBRARY} expat dl z m)

# Only install if installation directory has been defined
if(DEFINED INSTALL_DIR_DEFINED)
message(STATUS "Installing utility executable: ${execName}")
# Install into bin/utils dir
install(TARGETS ${execName} RUNTIME DESTINATION bin/utils)
endif()
endforeach()

# Add the C++ tests/examples
if(MAKE_EXAMPLES)
foreach(fileName ${TEST})
Expand Down
55 changes: 26 additions & 29 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,40 +1,50 @@
# **EVIO 6 SOFTWARE PACKAGE**

EVIO stands for EVent Input/Output, a unique data format developed by Jefferson Lab.
It was created by the Data Acquisition (DAQ) group and is maintained by the
Experimental Physics Software and Computing Infrastructure (EPSCI) group at Thomas
Jefferson National Accelerator Facility (JLab).
EVIO stands for EVent Input/Output, a unique data format developed by Jefferson Lab used by typical detector readout systems at the lab. This software repository allows one to read & write `.evio` and `.ev` format data, within either a C/C++ or Java programming environment.

This software repository allows one to read & write `.evio` and `.ev` format data,
within either a C/C++ or Java programming environment.
# **Useful Links**

Documentation on GitHub:

* [All Links](https://jeffersonlab.github.io/evio)
* [User's Guide PDF](https://jeffersonlab.github.io/evio/doc-6.0/users_guide/evio_Users_Guide.pdf)
* [EVIO Data Format Reference](https://jeffersonlab.github.io/evio/doc-6.0/format_guide/evio_Formats.pdf)

Software Library Documentation:

* [Javadoc for Java Library](https://jeffersonlab.github.io/evio/doc-6.0/javadoc/index.html)
* [Doxygen for C Library](https://jeffersonlab.github.io/evio/doc-6.0/doxygen/C/html/index.html)
* [Doxygen for C++ Libary](https://jeffersonlab.github.io/evio/doc-6.0/doxygen/CC/html/index.html)

# **Getting Started**

## **C/C++ Library**

To build C/C++ code from this repository:
The C and C++ libraries are build using `cmake`. To build C/C++ code from this repository:

git clone https://github.com/JeffersonLab/evio/
cd evio; mkdir build
cmake -S . -B build
cmake --build build --parallel
cmake --build build --target install --parallel

Note that during the cmake configure step (first of two `cmake` commands above), one can
toggle the following special flags:
Note that during the cmake configure step (first of two `cmake` commands above), one can also include the following special flags:

* `C_ONLY` : build C lib only, skip C++ (default `-DC_ONLY=0`)
* `MAKE_EXAMPLES`: build example/test programs (default `-DMAKE_EXAMPLES=0`)
* `USE_FILESYSTEMLIB`: ue C++17 <filesystem> instead of Boost (default `-DUSE_FILESYSTEMLIB=0`)
* `DISRUPTOR_FETCH`: allow CMake to download Disruptor if not found (default `-DDISRUPTOR_FETCH=1`)
* `CODA_INSTALL`: installs in this base directory. If not used,
then the env variable $CODA location is next checked. Otherwise defaults to \${CMAKE_HOST_SYSTEM_NAME}-\${CMAKE_HOST_SYSTEM_PROCESSOR}, typically something like `[evio_directory]/Linux-x86_64`.

One can still also use `scons` instead of cmake to build the evio C/C++ library, though this feature
will not be supported in future releases.

### Prerequisites

C++ 17 or higher, `cmake`, `lz4`, `boost_system`, `boost_thread`, and `boost_chrono`. If LZ4 is not
already configured, it can be installed from [LZ4 on github](https://github.com/lz4/lz4). The boost
libraries are typically system-specific.
C++ 17 or higher, `cmake`, `lz4`, `boost_system`, `boost_thread`, and `boost_chrono`. Compilation can
be done using `clang` or `gcc` (gcc 11 or higher recommended). If LZ4 is not
already configured, it can be installed from [LZ4 on github](https://github.com/lz4/lz4). Installation of boost
libraries are typically system-specific (e.g. using a command like `yum`, `dbn`, `rpm`, `apt-get`, etc.).

## **Java Library**

Expand All @@ -57,23 +67,12 @@ Requires Maven (`mvn`) and an installation of Java on your system.
**Running on "ifarm" at JLab will not work unless you install java yourself**. Note that the default java versions on the farm will be too old to
work. See downloads from [OpenJDK](https://openjdk.org/install/) or [Oracle](https://www.oracle.com/java/technologies/javase/jdk17-archive-downloads.html).

-----------------------------

# **Useful Links**

----------------------------
# **Further Information**

Documentation on GitHub:

* [All Documentation](https://jeffersonlab.github.io/evio)
* [User's Guide PDF](https://jeffersonlab.github.io/evio/doc-6.0/users_guide/evio_Users_Guide.pdf)
* [EVIO Data Format Reference](https://jeffersonlab.github.io/evio/doc-6.0/format_guide/evio_Formats.pdf)
The EVIO package was created by the Data Acquisition (DAQ) group and is maintained by the Experimental Physics Software and Computing Infrastructure (EPSCI) group at the Thomas Jefferson National Accelerator Facility (JLab). It has been developed by many authors over the years.

Software Library Documentation:

* [Javadoc for Java Library](https://jeffersonlab.github.io/evio/doc-6.0/javadoc/index.html)
* [Doxygen for C Library](https://jeffersonlab.github.io/evio/doc-6.0/doxygen/C/html/index.html)
* [Doxygen for C++ Libary](https://jeffersonlab.github.io/evio/doc-6.0/doxygen/CC/html/index.html)

Other Links:
* [EVIO Event Viewer on GitHub](https://github.com/JeffersonLab/JEventViewer)
Expand All @@ -86,10 +85,8 @@ well as the software used to read and write to these respective `.evio` and `.hi
More information on the HIPO data format can be found at https://github.com/gavalian/hipo,
or from the CLAS12 Software Project Coordinator.

----------------------------
Contact: Jon Zarling (jzarling@jlab.org)

# **Copyright**

----------------------------

For any issues regarding use and copyright, read the [license](LICENSE.txt) file.
4 changes: 2 additions & 2 deletions java/jars/README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
# **Java JARs Folder**

This folder contains any jar file dependencies required by the EVIO Java library that are not retrieved directly from the Maven repository. At present, only the disruptor library needs to be added from here.
This folder contains jar files used for executing EVIO code using the Java API. The main jar file was made using Java 17.

Note that the disruptor 4.0.0 jar file included comes from a [JeffersonLab fork](https://github.com/JeffersonLab/disruptor) of the original lmax Java library. This forked repository adds an additional function (SpinCountBackoffWaitStrategy) that is required in the evio Java Library.
It also includes dependencies required by the EVIO Java library that are not retrieved directly from the Maven repository. At present, only the disruptor dependency needs to be added from here. Note that the disruptor 4.0.0 jar file included comes from a [JeffersonLab fork](https://github.com/JeffersonLab/disruptor) of the original lmax Java library. This forked repository adds an additional function (SpinCountBackoffWaitStrategy) that is required in the evio Java Library.
3 changes: 2 additions & 1 deletion src/README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,5 +5,6 @@
| [libsrc](libsrc) | EVIO C library |
| [libsrc++](libsrc++) | EVIO C++ library |
| [main/java](main/java) | EVIO Java Library |
| [test](test) | For internal testing of Java, C, C++ libraries. |
| [test](test) | For internal testing of Java, C, C++ libraries. |
| [utils](utils) | Standalone programs, e.g. utilities to merge files, convert formats, attempt recovery, etc. |

6 changes: 4 additions & 2 deletions src/libsrc++/EventParser.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -227,9 +227,11 @@ namespace evio {
// --which will be interpreted by the various "get data" methods.
auto & bytes = structure->getRawBytes();
ByteOrder byteOrder = structure->getByteOrder();

if (bytes.empty()) {
throw EvioException("Null data in structure");
// throw EvioException("Null data in structure");
// printf("WARNING: no data inside structure! Skipping... \n");
// printf(" structure %s \n", structure->getHeader()->toString().c_str());
return;
}

size_t length = bytes.size();
Expand Down
10 changes: 6 additions & 4 deletions src/libsrc++/EvioReaderV4.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1090,7 +1090,7 @@ namespace evio {
uint32_t eventDataSizeBytes = 4*(length - 1);

try {
auto *bytes = new uint8_t[eventDataSizeBytes];
auto bytes = std::vector<uint8_t>(eventDataSizeBytes);

uint32_t bytesToGo = eventDataSizeBytes;
uint32_t offset = 0;
Expand All @@ -1106,7 +1106,7 @@ namespace evio {
blkBytesRemaining : bytesToGo;

// Read in bytes remaining in internal buffer
byteBuffer->getBytes(bytes + offset, bytesToReadNow);
byteBuffer->getBytes(bytes.data() + offset, bytesToReadNow);
offset += bytesToReadNow;
bytesToGo -= bytesToReadNow;
blkBytesRemaining -= bytesToReadNow;
Expand All @@ -1123,12 +1123,14 @@ namespace evio {
blkBytesRemaining = blockBytesRemaining();
}
}


}

// Last (perhaps only) read
byteBuffer->getBytes(bytes + offset, bytesToGo);
byteBuffer->getBytes(bytes.data() + offset, bytesToGo);
//std::cout << "nextEvent: eventDataSizeByte = " << eventDataSizeBytes << std::endl;
event->setRawBytes(bytes, eventDataSizeBytes);
event->setRawBytes(bytes.data(), eventDataSizeBytes);
event->setByteOrder(byteOrder); // add this to track endianness, timmer
// Don't worry about dictionaries here as version must be 1-3
event->setEventNumber(++eventNumber);
Expand Down
1 change: 1 addition & 0 deletions src/main/java/org/jlab/coda/jevio/EvioReader.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -215,6 +215,7 @@ public EvioReader(File file, boolean checkRecNumSeq, boolean sequential, boolean

// Parse file header to find the file's endianness & evio version #
if (findEvioVersion() != ReadStatus.SUCCESS) {
rFile.close();
throw new EvioException("Failed reading first block header");
}

Expand Down
2 changes: 1 addition & 1 deletion src/main/java/org/jlab/coda/jevio/EvioReaderUnsyncV4.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1046,7 +1046,7 @@ else if (bytesInBuf % 32768 == 0) {
// Check block size, attempt to recover if flag set
// (otherwise return exception with a hint to set flag)
// System.out.println("blkSize BEFORE = " + blkSize);
if(doHeaderRecoveryCheck && fileSize - fileChannel.position() >= 10*4) {
if(doHeaderRecoveryCheck && (fileSize - fileChannel.position()) >= 10*4 && fileChannel.position() > 20*4) {

int expectedMagicPos = 27; // in words
int words_to_skip = 0; // words_to_skip = foundMagicPos - expectedMagicPos
Expand Down
6 changes: 6 additions & 0 deletions src/test/README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
# **Test Programs**

These programs are used for continuous integration (CI) tests. As such,
they may not be the most useful reference programs for users. Essentially,
they test the various C++ and Java APIs to ensure that we can write some
simple dummy events to an evio file and read back expected values.
Loading