All my current code:
import tabula
pdfpath= "Testpdfs/HSA certCut.pdf"
sbc = tabula.read_pdf(pdfpath, stream=True, pages=4, format="CSV")[0]
print(sbc)
I have a fresh install of python3 and the latest JDK for ARM64.
When running, i get this error:
# A fatal error has been detected by the Java Runtime Environment:
#
# SIGBUS (0xa) at pc=0x000000011b2ad34c, pid=75744, tid=259
#
# JRE version: (22.0+36) (build )
# Java VM: Java HotSpot(TM) 64-Bit Server VM (22+36-2370, mixed mode, sharing, tiered, compressed oops, compressed class ptrs, g1 gc, bsd-aarch64)
# Problematic frame:
# V [libjvm.dylib+0x45934c] CodeHeap::allocate(unsigned long)+0x1a4
#
# No core dump will be written. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
#
# An error report file with more information is saved as:
# /Users/dmesser3/Desktop/tabulapy Tests/hs_err_pid75744.log
#
I don't know what is going wrong and I can't seem to find a fix. Any help is appreciated. See error log below.
#
# A fatal error has been detected by the Java Runtime Environment:
#
# SIGBUS (0xa) at pc=0x000000011b2ad34c, pid=75744, tid=259
#
# JRE version: (22.0+36) (build )
# Java VM: Java HotSpot(TM) 64-Bit Server VM (22+36-2370, mixed mode, sharing, tiered, compressed oops, compressed class ptrs, g1 gc, bsd-aarch64)
# Problematic frame:
# V [libjvm.dylib+0x45934c] CodeHeap::allocate(unsigned long)+0x1a4
#
# No core dump will be written. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
#
#
--------------- S U M M A R Y ------------
Command Line: -Djava.awt.headless=true -Dfile.encoding=UTF8
Host: "MacBookPro18,2" arm64, 10 cores, 64G, Darwin 23.4.0, macOS 14.4 (23E214)
Time: Thu Mar 21 10:59:40 2024 EDT elapsed time: 0.042656 seconds (0d 0h 0m 0s)
--------------- T H R E A D ---------------
Current thread (0x0000000156d36200): JavaThread "Unknown thread" [_thread_in_vm, id=259, stack(0x000000016e5c0000,0x000000016f5c0000) (16384K)]
Stack: [0x000000016e5c0000,0x000000016f5c0000], sp=0x000000016f5bd160, free space=16372k
Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
V [libjvm.dylib+0x45934c] CodeHeap::allocate(unsigned long)+0x1a4
V [libjvm.dylib+0x2781fc] CodeCache::allocate(unsigned int, CodeBlobType, bool, CodeBlobType)+0xa0
V [libjvm.dylib+0x26f590] BufferBlob::create(char const*, unsigned int)+0xf0
V [libjvm.dylib+0x935764] initialize_stubs(StubCodeGenerator::StubsKind, int, int, char const*, char const*, char const*)+0x9c
V [libjvm.dylib+0x9359ec] initial_stubs_init()+0x44
V [libjvm.dylib+0x4863f0] init_globals()+0x2c
V [libjvm.dylib+0x993f58] Threads::create_vm(JavaVMInitArgs*, bool*)+0x260
V [libjvm.dylib+0x53e08c] JNI_CreateJavaVM+0x68
C [_jpype.cpython-39-darwin.so+0x10e84] JPContext::startJVM(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&, std::__1::vector<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>, std::__1::allocator<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>>> const&, bool, bool, bool)+0xd0
C [_jpype.cpython-39-darwin.so+0x3c730] PyJPModule_startup(_object*, _object*)+0x1f8
C [Python3+0x83d64] PyCFunction_GetFlags+0x338
C [Python3+0x407c8] _PyObject_MakeTpCall+0x168
C [Python3+0x112664] _PyEval_EvalFrameDefault+0x8784
C [Python3+0x10f754] _PyEval_EvalFrameDefault+0x5874
C [Python3+0x1134ac] _PyEval_EvalFrameDefault+0x95cc
C [Python3+0x40f58] _PyFunction_Vectorcall+0xec
C [Python3+0x40c00] PyVectorcall_Call+0x90
C [Python3+0x10fa28] _PyEval_EvalFrameDefault+0x5b48
C [Python3+0x1134ac] _PyEval_EvalFrameDefault+0x95cc
C [Python3+0x40f58] _PyFunction_Vectorcall+0xec
C [Python3+0x4056c] _PyObject_FastCallDictTstate+0x8c
C [Python3+0x41338] _PyObject_Call_Prepend+0x94
C [Python3+0xa575c] _PyType_Lookup+0x94a0
C [Python3+0x9cbb8] _PyType_Lookup+0x8fc
C [Python3+0x407c8] _PyObject_MakeTpCall+0x168
C [Python3+0x112664] _PyEval_EvalFrameDefault+0x8784
C [Python3+0x10f84c] _PyEval_EvalFrameDefault+0x596c
C [Python3+0x1134ac] _PyEval_EvalFrameDefault+0x95cc
C [Python3+0x40f58] _PyFunction_Vectorcall+0xec
C [Python3+0x112604] _PyEval_EvalFrameDefault+0x8724
C [Python3+0x10f84c] _PyEval_EvalFrameDefault+0x596c
C [Python3+0x1134ac] _PyEval_EvalFrameDefault+0x95cc
C [Python3+0x40f58] _PyFunction_Vectorcall+0xec
C [Python3+0x112604] _PyEval_EvalFrameDefault+0x8724
C [Python3+0x10f84c] _PyEval_EvalFrameDefault+0x596c
C [Python3+0x1134ac] _PyEval_EvalFrameDefault+0x95cc
C [Python3+0x109e18] PyEval_EvalCode+0x50
C [Python3+0x14de54] PyParser_ASTFromStringObject+0x1f4
C [Python3+0x14e028] PyRun_FileExFlags+0x154
C [Python3+0x14c154] PyRun_SimpleFileExFlags+0x334
C [Python3+0x1692b0] Py_RunMain+0x644
C [Python3+0x169720] Py_Main+0x174
C [Python3+0x1697c0] Py_BytesMain+0x28
C [dyld+0x60e0] start+0x938
siginfo: si_signo: 10 (SIGBUS), si_code: 1 (BUS_ADRALN), si_addr: 0x0000000176fe000
--------------- P R O C E S S ---------------
Threads class SMR info:
_java_thread_list=0x000000011bb11bd8, length=0, elements={
}
Java Threads: ( => current thread )
Total: 0
Other Threads:
=>0x0000000156d36200 (exited) JavaThread "Unknown thread" [_thread_in_vm, id=259, stack(0x000000016e5c0000,0x000000016f5c0000) (16384K)]
Total: 1
Threads with active compile tasks:
Total: 0
VM state: not at safepoint (not fully initialized)
VM Mutex/Monitor currently owned by a thread: ([mutex/lock_event])
[0x000000011bb6cd58] CodeCache_lock - owner thread: 0x0000000156d36200
Heap address: 0x0000000000000000, size: 0 MB, Compressed Oops mode: 32-bit
CDS archive(s) mapped at: [0x0000000000000000-0x0000000000000000-0x0000000000000000), size 0, SharedBaseAddress: 0x0000000800000000, ArchiveRelocationMode: 1.
Narrow klass base: 0x0000000000000000, Narrow klass shift: 0, Narrow klass range: 0x0
GC Precious Log:
<Not initialized>
Dll operation events (1 events):
Event: 0.041 Loaded shared library /Library/Java/JavaVirtualMachines/jdk-22.jdk/Contents/Home/lib/libjava.dylib
Events (1 events):
Event: 0.009 Protecting memory [0x000000016e5c0000,0x000000016e5cc000] with protection modes 0
VM Arguments:
jvm_args: -Djava.awt.headless=true -Dfile.encoding=UTF8
java_command: <unknown>
java_class_path (initial): /Users/dmesser3/Library/Python/3.9/lib/python/site-packages/tabula/tabula-1.0.5-jar-with-dependencies.jar
Launcher Type: generic
[Global flags]
intx CICompilerCount = 4 {product} {ergonomic}
uint ConcGCThreads = 2 {product} {ergonomic}
uint G1ConcRefinementThreads = 9 {product} {ergonomic}
size_t InitialHeapSize = 1073741824 {product} {ergonomic}
size_t MarkStackSize = 4194304 {product} {ergonomic}
size_t MaxHeapSize = 17179869184 {product} {ergonomic}
size_t MinHeapSize = 6815736 {product} {ergonomic}
uintx NonNMethodCodeHeapSize = 5839564 {pd product} {ergonomic}
uintx NonProfiledCodeHeapSize = 122909338 {pd product} {ergonomic}
uintx ProfiledCodeHeapSize = 122909338 {pd product} {ergonomic}
uintx ReservedCodeCacheSize = 251658240 {pd product} {ergonomic}
bool SegmentedCodeCache = true {product} {ergonomic}
bool UseCompressedOops = true {product lp64_product} {ergonomic}
bool UseG1GC = true {product} {ergonomic}
bool UseNUMA = false {product} {ergonomic}
bool UseNUMAInterleaving = false {product} {ergonomic}
Logging:
Log output configuration:
#0: stdout all=warning uptime,level,tags foldmultilines=false
#1: stderr all=off uptime,level,tags foldmultilines=false
Environment Variables:
JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk-22.jdk/Contents/Home
PATH=/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/local/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/bin:/var/run/com.apple.security.cryptexd/codex.system/bootstrap/usr/appleinternal/bin:/opt/homebrew/bin:/opt/homebrew/sbin
SHELL=/bin/zsh
LANG=en_US.UTF-8
TERM=xterm-256color
TMPDIR=/var/folders/hd/tm_c7_6n6dzgb384j3rs7j800000gq/T/
Active Locale:
LC_ALL=C/en_US.UTF-8/C/C/C/C
LC_COLLATE=C
LC_CTYPE=en_US.UTF-8
LC_MESSAGES=C
LC_MONETARY=C
LC_NUMERIC=C
LC_TIME=C
Signal Handlers:
SIGSEGV: crash_handler in libjvm.dylib, mask=11100110000111110111111111111111, flags=SA_ONSTACK|SA_RESTART|SA_SIGINFO, unblocked
SIGBUS: crash_handler in libjvm.dylib, mask=11100110000111110111111111111111, flags=SA_RESTART|SA_SIGINFO, unblocked
SIGFPE: crash_handler in libjvm.dylib, mask=11100110000111110111111111111111, flags=SA_RESTART|SA_SIGINFO, unblocked
SIGPIPE: javaSignalHandler in libjvm.dylib, mask=11100110000111110111111111111111, flags=SA_RESTART|SA_SIGINFO, blocked
SIGXFSZ: javaSignalHandler in libjvm.dylib, mask=11100110000111110111111111111111, flags=SA_RESTART|SA_SIGINFO, blocked
SIGILL: crash_handler in libjvm.dylib, mask=11100110000111110111111111111111, flags=SA_RESTART|SA_SIGINFO, unblocked
SIGUSR2: SR_handler in libjvm.dylib, mask=00000000000000000000000000000000, flags=SA_RESTART|SA_SIGINFO, blocked
SIGHUP: SIG_DFL, mask=00000000000000000000000000000000, flags=none, blocked
SIGINT: PyInit__signal+1448 in Python3, mask=00000000000000000000000000000000, flags=none, blocked
SIGTERM: SIG_DFL, mask=00000000000000000000000000000000, flags=SA_RESTART, blocked
SIGQUIT: UserHandler in libjvm.dylib, mask=11100110000111110111111111111111, flags=SA_RESTART|SA_SIGINFO, blocked
SIGTRAP: crash_handler in libjvm.dylib, mask=11100110000111110111111111111111, flags=SA_RESTART|SA_SIGINFO, unblocked
Periodic native trim disabled
--------------- S Y S T E M ---------------
OS:
uname: Darwin 23.4.0 Darwin Kernel Version 23.4.0: Wed Feb 21 21:44:43 PST 2024; root:xnu-10063.101.15~2/RELEASE_ARM64_T6000 arm64
OS uptime: 2 days 18:43 hours
rlimit (soft/hard): STACK 8176k/65520k , CORE 0k/infinity , NPROC 10666/16000 , NOFILE 10240/infinity , AS infinity/infinity , CPU infinity/infinity , DATA infinity/infinity , FSIZE infinity/infinity , MEMLOCK infinity/infinity , RSS infinity/infinity
load average: 5.23 3.03 2.73
CPU: total 10 (initial active 10) 0x61:0x0:0x1b588bb3:0, fp, asimd, aes, pmull, sha1, sha256, crc32, lse, sha3, sha512
machdep.cpu.brand_string:Apple M1 Max
hw.cachelinesize:128
hw.l1icachesize:131072
hw.l1dcachesize:65536
hw.l2cachesize:4194304
Memory: 16k page, physical 67108864k(26293056k free), swap 0k(0k free)
vm_info: Java HotSpot(TM) 64-Bit Server VM (22+36-2370) for bsd-aarch64 JRE (22+36-2370), built on 2024-02-15T22:15:19Z by "mach5one" with clang Apple LLVM 14.0.3 (clang-1403.0.22.14.1)
END.
I ensured my path variables are correct. I ensured I have the proper installations of python and JDK. I homebrewed python3, and just used the dmg downloader for ARM64 JDK 22.