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Problems using gadd to sum GRUT histogram files - ROOT6 #118

Closed placebosarah closed 7 years ago

placebosarah commented 8 years ago

Hi all, I'm having difficulties adding histograms using gadd to create sum histograms (*). It seems that there could be some problems with the library linkage using ROOT 6 from what I can tell from ROOT's online forum (https://root.cern.ch/phpBB3/viewtopic.php?t=20923).

I'm using ROOT 6.06/08 and the latest GRUTinizer version, with GCC 4.8.5. Any suggestions on how to fix this?

Thanks, Sarah

(*) gadd sumhist_run0033-5.root hist_run0033_test.root hist_run0034_test.root hist_run0035_test.root gadd Target file: sumhist_run0033-5.root gadd Source file 1: hist_run0033_test.root Warning in TClass::Init: no dictionary for class GH1D is available Warning in TClass::Init: no dictionary for class GH2D is available Warning in TClass::Init: no dictionary for class GH2Base is available gadd Source file 2: hist_run0034_test.root gadd Source file 3: hist_run0035_test.root gadd Target path: sumhist_run0033-5.root:/

Error in TBufferFile::ReadClassBuffer: Could not find the StreamerInfo for version 7 of the class TNamed, object skipped at offset 81 Error in TBufferFile::CheckByteCount: object of class TNamed read too few bytes: 2 instead of 524 Error in TBufferFile::ReadClassBuffer: class: TAttFill, attempting to access a wrong version: 2002, object skipped at offset 607 Error in TBufferFile::CheckByteCount: object of class TH1 read too few bytes: 767 instead of 16550 Error in TBufferFile::CheckByteCount: object of class TH1D read too few bytes: 16560 instead of 16572 Error in TFileMerger::MergeRecursive: TKey and object retrieve disagree on type (GH1D vs TH1D). Continuing with TH1D.

(similar errors continue for some time...)

pcbend commented 8 years ago

So this is a problem seeing the dictionaries. Did you source the thisgrut.sh file first or have the proper paths setup in in your .bashrc? What happens if you just type grutinizer on the command line?

On Tue, Oct 18, 2016 at 9:51 AM, placebosarah notifications@github.com wrote:

Hi all, I'm having difficulties adding histograms using gadd to create sum histograms (*). It seems that there could be some problems with the library linkage using ROOT 6 from what I can tell from ROOT's online forum ( https://root.cern.ch/phpBB3/viewtopic.php?t=20923).

I'm using ROOT 6.06/08 and the latest GRUTinizer version, with GCC 4.8.5. Any suggestions on how to fix this?

Thanks,

Sarah

(*) gadd sumhist_run0033-5.root hist_run0033_test.root hist_run0034_test.root hist_run0035_test.root gadd Target file: sumhist_run0033-5.root gadd Source file 1: hist_run0033_test.root Warning in TClass::Init: no dictionary for class GH1D is available Warning in TClass::Init: no dictionary for class GH2D is available Warning in TClass::Init: no dictionary for class GH2Base is available gadd Source file 2: hist_run0034_test.root gadd Source file 3: hist_run0035_test.root gadd Target path: sumhist_run0033-5.root:/

Error in TBufferFile::ReadClassBuffer: Could not find the StreamerInfo for version 7 of the class TNamed, object skipped at offset 81 Error in TBufferFile::CheckByteCount: object of class TNamed read too few bytes: 2 instead of 524 Error in TBufferFile::ReadClassBuffer: class: TAttFill, attempting to access a wrong version: 2002, object skipped at offset 607 Error in TBufferFile::CheckByteCount: object of class TH1 read too few bytes: 767 instead of 16550 Error in TBufferFile::CheckByteCount: object of class TH1D read too few bytes: 16560 instead of 16572 Error in TFileMerger::MergeRecursive: TKey and object retrieve disagree on type (GH1D vs TH1D). Continuing with TH1D. (similar errors continue for some time...)

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placebosarah commented 8 years ago

I source thisgrut.sh beforehand, and I can use grutinizer from the command line successfully.

pcbend commented 8 years ago

ok, I am working on reproducing the error locally. I'll let you know what I find soon.

On Wed, Oct 19, 2016 at 10:53 AM, placebosarah notifications@github.com wrote:

I source thisgrut.sh beforehand, and I can use grutinizer from the command line successfully.

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pcbend commented 8 years ago

Just out of curiosity, can you see/display the histograms in the each file if you open them on there own?

On Wed, Oct 19, 2016 at 10:55 AM, Peter pcbend@gmail.com wrote:

ok, I am working on reproducing the error locally. I'll let you know what I find soon.

On Wed, Oct 19, 2016 at 10:53 AM, placebosarah notifications@github.com wrote:

I source thisgrut.sh beforehand, and I can use grutinizer from the command line successfully.

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placebosarah commented 8 years ago

Yes, I can see and display histograms when each file is opened individually. The problems only seem to occur when using gadd.

pcbend commented 8 years ago

can you try:

gadd_fast.py -f sumhist_run0033-5.root hist_run0033_test.root hist_run0034_test.root hist_run0035_test.root

and let me know how it works?

On Wed, Oct 19, 2016 at 11:01 AM, placebosarah notifications@github.com wrote:

Yes, I can see and display histograms when each file is opened individually. The problems only seem to occur when using gadd.

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placebosarah commented 8 years ago

Failed again, with exit status -6 ?

gadd_fast.py -f sumhist_run0033-5.root hist_run0033_test.root hist_run0034_test.root hist_run0035_test.root gadd -f /tmp/tmpc7g2k9vt/merge1.root hist_run0033_test.root hist_run0034_test.root hist_run0035_test.root

Traceback (most recent call last): File "/scratch2/MSU/GRUTinizer/GRUTinizer/bin/gadd_fast.py", line 115, in sys.exit(main()) File "/scratch2/MSU/GRUTinizer/GRUTinizer/bin/gadd_fast.py", line 110, in main merger.merge(args.input_files, args.output_file) File "/scratch2/MSU/GRUTinizer/GRUTinizer/bin/gadd_fast.py", line 70, in merge print(' '.join(['mv', to_merge[0].result(), output_file])) File "/usr/lib64/python3.4/concurrent/futures/_base.py", line 402, in result return self.get_result() File "/usr/lib64/python3.4/concurrent/futures/_base.py", line 354, in get_result raise self._exception File "/usr/lib64/python3.4/concurrent/futures/thread.py", line 54, in run result = self.fn(_self.args, *_self.kwargs) File "/scratch2/MSU/GRUTinizer/GRUTinizer/bin/gadd_fast.py", line 75, in _submerge call_gadd(input_files, output_file, self.gadd_args) File "/scratch2/MSU/GRUTinizer/GRUTinizer/bin/gadd_fast.py", line 24, in call_gadd subprocess.check_call(args, stdout=devnull, stderr=devnull) File "/usr/lib64/python3.4/subprocess.py", line 561, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['gadd', '-f', '/tmp/tmpc7g2k9vt/merge1.root', 'hist_run0033_test.root', 'hist_run0034_test.root', 'hist_run0035_test.root']' returned non-zero exit status -6

pcbend commented 8 years ago

I have failed to reproduce this locally. How big are the hist files you are trying to gadd? Any chance you could mail me two of them?

On Oct 19, 2016 11:46 AM, "placebosarah" notifications@github.com wrote:

Failed again, with exit status -6 ?

gadd_fast.py -f sumhist_run0033-5.root hist_run0033_test.root hist_run0034_test.root hist_run0035_test.root gadd -f /tmp/tmpc7g2k9vt/merge1.root hist_run0033_test.root hist_run0034_test.root hist_run0035_test.root

Traceback (most recent call last): File "/scratch2/MSU/GRUTinizer/GRUTinizer/bin/gadd_fast.py", line 115, in sys.exit(main()) File "/scratch2/MSU/GRUTinizer/GRUTinizer/bin/gadd_fast.py", line 110, in main merger.merge(args.input_files, args.output_file) File "/scratch2/MSU/GRUTinizer/GRUTinizer/bin/gadd_fast.py", line 70, in merge print(' '.join(['mv', to_merge[0].result(), output_file])) File "/usr/lib64/python3.4/concurrent/futures/_base.py", line 402, in result return self.get_result() File "/usr/lib64/python3.4/concurrent/futures/_base.py", line 354, in get_result raise self._exception File "/usr/lib64/python3.4/concurrent/futures/thread.py", line 54, in run result = self.fn(_self.args, *_self.kwargs) File "/scratch2/MSU/GRUTinizer/GRUTinizer/bin/gadd_fast.py", line 75, in _submerge call_gadd(input_files, output_file, self.gadd_args) File "/scratch2/MSU/GRUTinizer/GRUTinizer/bin/gadd_fast.py", line 24, in call_gadd subprocess.check_call(args, stdout=devnull, stderr=devnull) File "/usr/lib64/python3.4/subprocess.py", line 561, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['gadd', '-f', '/tmp/tmpc7g2k9vt/merge1.root', 'hist_run0033_test.root', 'hist_run0034_test.root', 'hist_run0035_test.root']' returned non-zero exit status -6

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pcbend commented 8 years ago

Or put them some place I can grab them?

On Oct 19, 2016 11:46 AM, "placebosarah" notifications@github.com wrote:

Failed again, with exit status -6 ?

gadd_fast.py -f sumhist_run0033-5.root hist_run0033_test.root hist_run0034_test.root hist_run0035_test.root gadd -f /tmp/tmpc7g2k9vt/merge1.root hist_run0033_test.root hist_run0034_test.root hist_run0035_test.root

Traceback (most recent call last): File "/scratch2/MSU/GRUTinizer/GRUTinizer/bin/gadd_fast.py", line 115, in sys.exit(main()) File "/scratch2/MSU/GRUTinizer/GRUTinizer/bin/gadd_fast.py", line 110, in main merger.merge(args.input_files, args.output_file) File "/scratch2/MSU/GRUTinizer/GRUTinizer/bin/gadd_fast.py", line 70, in merge print(' '.join(['mv', to_merge[0].result(), output_file])) File "/usr/lib64/python3.4/concurrent/futures/_base.py", line 402, in result return self.get_result() File "/usr/lib64/python3.4/concurrent/futures/_base.py", line 354, in get_result raise self._exception File "/usr/lib64/python3.4/concurrent/futures/thread.py", line 54, in run result = self.fn(_self.args, *_self.kwargs) File "/scratch2/MSU/GRUTinizer/GRUTinizer/bin/gadd_fast.py", line 75, in _submerge call_gadd(input_files, output_file, self.gadd_args) File "/scratch2/MSU/GRUTinizer/GRUTinizer/bin/gadd_fast.py", line 24, in call_gadd subprocess.check_call(args, stdout=devnull, stderr=devnull) File "/usr/lib64/python3.4/subprocess.py", line 561, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['gadd', '-f', '/tmp/tmpc7g2k9vt/merge1.root', 'hist_run0033_test.root', 'hist_run0034_test.root', 'hist_run0035_test.root']' returned non-zero exit status -6

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placebosarah commented 8 years ago

The histogram files are about ~6MB each- I've sent you a zipped file by email with the files I've been using.

placebosarah commented 8 years ago

With the latest updates to gadd, the problem still persists. The following are my environment variables, are there any quirks that might cause the issue?

$ echo $ROOTSYS /usr/share/root $ echo $PATH /scratch2/MSU/GRUTinizer/GRUTinizer/bin:/usr/share/applications:/opt/sge/bin:/opt/sge/bin/lx-amd64:/usr/lib64/qt-3.3/bin:/opt/mendeleydesktop/bin:/opt/matlab-R2015a/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/opt/pgi/linux86-64/15.5/bin:/opt/rw05-3 $ echo $LD_LIBRARY_PATH /scratch2/MSU/GRUTinizer/GRUTinizer/lib:/usr/lib64/root $ echo $ROOT_INCLUDE_PATH /scratch2/MSU/GRUTinizer/GRUTinizer/include:/usr/include/root

$ gadd -f sumhist_run0033-5.root hist_run0033_test.root hist_run0034_test.root hist_run0035_test.root gadd Target file: sumhist_run0033-5.root gadd Source file 1: hist_run0033_test.root Warning in TClass::Init: no dictionary for class GH1D is available Warning in TClass::Init: no dictionary for class GH2D is available Warning in TClass::Init: no dictionary for class GH2Base is available gadd Source file 2: hist_run0034_test.root gadd Source file 3: hist_run0035_test.root gadd Target path: sumhist_run0033-5.root:/ Error in TBufferFile::ReadClassBuffer: Could not find the StreamerInfo for version 7 of the class TNamed, object skipped at offset 81 Error in TBufferFile::CheckByteCount: object of class TNamed read too few bytes: 2 instead of 524 Error in TBufferFile::ReadClassBuffer: class: TAttFill, attempting to access a wrong version: 2002, object skipped at offset 607 Error in TBufferFile::CheckByteCount: object of class TH1 read too few bytes: 767 instead of 16550 Error in TBufferFile::CheckByteCount: object of class TH1D read too few bytes: 16560 instead of 16572 Error in TFileMerger::MergeRecursive: TKey and object retrieve disagree on type (GH1D vs TH1D). Continuing with TH1D. Error in TBufferFile::ReadClassBuffer: Could not find the StreamerInfo for version 7 of the class TNamed, object skipped at offset 81 Error in TBufferFile::CheckByteCount: object of class TNamed read too few bytes: 2 instead of 524 Error in TBufferFile::ReadClassBuffer: class: TAttFill, attempting to access a wrong version: 2002, object skipped at offset 607 Error in TBufferFile::CheckByteCount: object of class TH1 read too few bytes: 767 instead of 16550 Error in TBufferFile::CheckByteCount: object of class TH1D read too few bytes: 16560 instead of 16572 Error in TBufferFile::ReadClassBuffer: Could not find the StreamerInfo for version 7 of the class TNamed, object skipped at offset 81 Error in TBufferFile::CheckByteCount: object of class TNamed read too few bytes: 2 instead of 524 Error in TBufferFile::ReadClassBuffer: class: TAttFill, attempting to access a wrong version: 2002, object skipped at offset 607 Error in TBufferFile::CheckByteCount: object of class TH1 read too few bytes: 767 instead of 16550 Error in TBufferFile::CheckByteCount: object of class TH1D read too few bytes: 16560 instead of 16572 gadd Target path: sumhist_run0033-5.root:/CRDC Error in TBufferFile::ReadClassBuffer: Could not find the StreamerInfo for version 7 of the class TNamed, object skipped at offset 65 Error in TBufferFile::CheckByteCount: object of class TNamed read too few bytes: 2 instead of 508 Error in TBufferFile::ReadClassBuffer: class: TAttFill, attempting to access a wrong version: 1002, object skipped at offset 575 Error in TBufferFile::CheckByteCount: object of class TH1 read too few bytes: 751 instead of 8534 Error in TBufferFile::CheckByteCount: object of class TH1D read too few bytes: 8544 instead of 8556 Error in TFileMerger::MergeRecursive: TKey and object retrieve disagree on type (GH1D vs TH1D). Continuing with TH1D. Error in TBufferFile::ReadClassBuffer: Could not find the StreamerInfo for version 7 of the class TNamed, object skipped at offset 65 Error in TBufferFile::CheckByteCount: object of class TNamed read too few bytes: 2 instead of 508 Error in TBufferFile::ReadClassBuffer: class: TAttFill, attempting to access a wrong version: 1002, object skipped at offset 575 Error in TBufferFile::CheckByteCount: object of class TH1 read too few bytes: 751 instead of 8534 Error in TBufferFile::CheckByteCount: object of class TH1D read too few bytes: 8544 instead of 8556 Error in TBufferFile::ReadClassBuffer: Could not find the StreamerInfo for version 7 of the class TNamed, object skipped at offset 65 Error in TBufferFile::CheckByteCount: object of class TNamed read too few bytes: 2 instead of 508 Error in TBufferFile::ReadClassBuffer: class: TAttFill, attempting to access a wrong version: 1002, object skipped at offset 575 Error in TBufferFile::CheckByteCount: object of class TH1 read too few bytes: 751 instead of 8534 Error in TBufferFile::CheckByteCount: object of class TH1D read too few bytes: 8544 instead of 8556 Error in TBufferFile::ReadClassBuffer: Could not find the StreamerInfo for version 7 of the class TNamed, object skipped at offset 65 Error in TBufferFile::CheckByteCount: object of class TNamed read too few bytes: 2 instead of 508 Error in TBufferFile::ReadClassBuffer: class: TAttFill, attempting to access a wrong version: 1002, object skipped at offset 575 Error in TBufferFile::CheckByteCount: object of class TH1 read too few bytes: 751 instead of 8534 Error in TBufferFile::CheckByteCount: object of class TH1D read too few bytes: 8544 instead of 8556 Error in TFileMerger::MergeRecursive: TKey and object retrieve disagree on type (GH1D vs TH1D). Continuing with TH1D. Error in TBufferFile::ReadClassBuffer: Could not find the StreamerInfo for version 7 of the class TNamed, object skipped at offset 65 Error in TBufferFile::CheckByteCount: object of class TNamed read too few bytes: 2 instead of 508 Error in TBufferFile::ReadClassBuffer: class: TAttFill, attempting to access a wrong version: 12002, object skipped at offset 575 Error in TBufferFile::ReadVersion: Could not find the StreamerInfo with a checksum of 0x0 for the class "TAttMarker" in hist_run0033_test.root. Error in TBufferFile::CheckByteCount: object of class TAttMarker read too few bytes: 6 instead of 1310720 Error in TBufferFile::CheckByteCount: Byte count probably corrupted around buffer position 575: 1310720 for a possible maximum of 96022 Error in TBufferFile::ReadBuffer1: class: TAttAxis, attempting to access a wrong version: 49, object skipped at offset 96617 Error in TBufferFile::ReadClassBuffer: class: TNamed, attempting to access a wrong version: 144, object skipped at offset 96689 Error in TBufferFile::CheckByteCount: object of class TH1 read too many bytes: 96767 instead of 96534 Warning in TBufferFile::CheckByteCount: TH1::Streamer() not in sync with data on file hist_run0033_test.root, fix Streamer() Error in TBufferFile::CheckByteCount: object of class TH1D read too few bytes: 96544 instead of 96556 Error in TFileMerger::MergeRecursive: TKey and object retrieve disagree on type (GH1D vs TH1D). Continuing with TH1D. Error in TBufferFile::ReadClassBuffer: Could not find the StreamerInfo for version 7 of the class TNamed, object skipped at offset 65 Error in TBufferFile::CheckByteCount: object of class TNamed read too few bytes: 2 instead of 508 Error in TBufferFile::ReadClassBuffer: class: TAttFill, attempting to access a wrong version: 12002, object skipped at offset 575 Error in TBufferFile::ReadVersion: Could not find the StreamerInfo with a checksum of 0x0 for the class "TAttMarker" in hist_run0034_test.root. Error in TBufferFile::CheckByteCount: object of class TAttMarker read too few bytes: 6 instead of 1048576 Error in TBufferFile::CheckByteCount: Byte count probably corrupted around buffer position 575: 1048576 for a possible maximum of 96022 Error in TBufferFile::ReadBuffer1: class: TAttAxis, attempting to access a wrong version: 49, object skipped at offset 96617 Error in TBufferFile::ReadClassBuffer: class: TNamed, attempting to access a wrong version: 176, object skipped at offset 96689 Error in TBufferFile::ReadBuffer1: class: TAttAxis, attempting to access a wrong version: 6124, object skipped at offset 96691 Error in TBufferFile::CheckByteCount: object of class TH1 read too many bytes: 96733 instead of 96534 Warning in TBufferFile::CheckByteCount: TH1::Streamer() not in sync with data on file hist_run0034_test.root, fix Streamer() Error in TBufferFile::CheckByteCount: object of class TH1D read too few bytes: 96544 instead of 96556 Error in TBufferFile::ReadClassBuffer: Could not find the StreamerInfo for version 7 of the class TNamed, object skipped at offset 65 Error in TBufferFile::CheckByteCount: object of class TNamed read too few bytes: 2 instead of 508 Error in TBufferFile::ReadClassBuffer: class: TAttFill, attempting to access a wrong version: 12002, object skipped at offset 575 Error in TBufferFile::ReadVersion: Could not find the StreamerInfo with a checksum of 0x0 for the class "TAttMarker" in hist_run0035_test.root. Error in TBufferFile::CheckByteCount: object of class TAttMarker read too few bytes: 6 instead of 1310720 Error in TBufferFile::CheckByteCount: Byte count probably corrupted around buffer position 575: 1310720 for a possible maximum of 96022 Error in TBufferFile::ReadBuffer1: class: TAttAxis, attempting to access a wrong version: 49, object skipped at offset 96617 Error in TBufferFile::ReadClassBuffer: class: TNamed, attempting to access a wrong version: 64, object skipped at offset 96689 Error in TBufferFile::ReadBuffer1: class: TAttAxis, attempting to access a wrong version: 12524, object skipped at offset 96691 Error in TBufferFile::CheckByteCount: object of class TH1 read too many bytes: 96733 instead of 96534 Warning in TBufferFile::CheckByteCount: TH1::Streamer() not in sync with data on file hist_run0035_test.root, fix Streamer() Error in TBufferFile::CheckByteCount: object of class TH1D read too few bytes: 96544 instead of 96556 Error in TBufferFile::ReadClassBuffer: Could not find the StreamerInfo for version 7 of the class TNamed, object skipped at offset 65 Error in TBufferFile::CheckByteCount: object of class TNamed read too few bytes: 2 instead of 508 Error in TBufferFile::ReadClassBuffer: class: TAttFill, attempting to access a wrong version: 12002, object skipped at offset 575 Error in TBufferFile::ReadVersion: Could not find the StreamerInfo with a checksum of 0x0 for the class "TAttMarker" in hist_run0033_test.root. Error in TBufferFile::CheckByteCount: object of class TAttMarker read too few bytes: 6 instead of 1310720 Error in TBufferFile::CheckByteCount: Byte count probably corrupted around buffer position 575: 1310720 for a possible maximum of 96022 Error in TBufferFile::ReadBuffer1: class: TAttAxis, attempting to access a wrong version: 49, object skipped at offset 96617 Error in TBufferFile::ReadClassBuffer: class: TNamed, attempting to access a wrong version: 144, object skipped at offset 96689 Error in TBufferFile::CheckByteCount: object of class TH1 read too many bytes: 96767 instead of 96534 Warning in TBufferFile::CheckByteCount: TH1::Streamer() not in sync with data on file hist_run0033_test.root, fix Streamer() Error in TBufferFile::CheckByteCount: object of class TH1D read too few bytes: 96544 instead of 96556 Error in TFileMerger::MergeRecursive: TKey and object retrieve disagree on type (GH1D vs TH1D). Continuing with TH1D. Error in TBufferFile::ReadClassBuffer: Could not find the StreamerInfo for version 4 of the class TH1, object skipped at offset 67 Error in TBufferFile::CheckByteCount: object of class TH1 read too few bytes: 2 instead of 548 Error in TFileMerger::MergeRecursive: TKey and object retrieve disagree on type (GH2D vs TH2D). Continuing with TH2D. Error in TBufferFile::ReadClassBuffer: Could not find the StreamerInfo for version 4 of the class TH1, object skipped at offset 67 Error in TBufferFile::CheckByteCount: object of class TH1 read too few bytes: 2 instead of 548 Error in TBufferFile::ReadClassBuffer: Could not find the StreamerInfo for version 4 of the class TH1, object skipped at offset 67 Error in TBufferFile::CheckByteCount: object of class TH1 read too few bytes: 2 instead of 548 Error in TBufferFile::ReadClassBuffer: Could not find the StreamerInfo for version 4 of the class TH1, object skipped at offset 67 Error in TBufferFile::CheckByteCount: object of class TH1 read too few bytes: 2 instead of 548 Error in TFileMerger::MergeRecursive: TKey and object retrieve disagree on type (GH2D vs TH2D). Continuing with TH2D. Error in TBufferFile::ReadClassBuffer: Could not find the StreamerInfo for version 7 of the class TNamed, object skipped at offset 65 Error in TBufferFile::CheckByteCount: object of class TNamed read too few bytes: 2 instead of 508 Error in TBufferFile::ReadClassBuffer: class: TAttFill, attempting to access a wrong version: 802, object skipped at offset 575 Error in TBufferFile::CheckByteCount: object of class TH1 read too few bytes: 751 instead of 6934 Error in TBufferFile::CheckByteCount: object of class TH1D read too few bytes: 6944 instead of 6956 Error in TFileMerger::MergeRecursive: TKey and object retrieve disagree on type (GH1D vs TH1D). Continuing with TH1D. Error in TBufferFile::ReadClassBuffer: Could not find the StreamerInfo for version 7 of the class TNamed, object skipped at offset 65 Error in TBufferFile::CheckByteCount: object of class TNamed read too few bytes: 2 instead of 508 Error in TBufferFile::ReadClassBuffer: class: TAttFill, attempting to access a wrong version: 802, object skipped at offset 575 Error in TBufferFile::CheckByteCount: object of class TH1 read too few bytes: 751 instead of 6934 Error in TBufferFile::CheckByteCount: object of class TH1D read too few bytes: 6944 instead of 6956 Error in TBufferFile::ReadClassBuffer: Could not find the StreamerInfo for version 7 of the class TNamed, object skipped at offset 65 Error in TBufferFile::CheckByteCount: object of class TNamed read too few bytes: 2 instead of 508 Error in TBufferFile::ReadClassBuffer: class: TAttFill, attempting to access a wrong version: 802, object skipped at offset 575 Error in TBufferFile::CheckByteCount: object of class TH1 read too few bytes: 751 instead of 6934 Error in TBufferFile::CheckByteCount: object of class TH1D read too few bytes: 6944 instead of 6956 Error in TBufferFile::ReadClassBuffer: Could not find the StreamerInfo for version 7 of the class TNamed, object skipped at offset 65 Error in TBufferFile::CheckByteCount: object of class TNamed read too few bytes: 2 instead of 508 Error in TBufferFile::ReadClassBuffer: class: TAttFill, attempting to access a wrong version: 802, object skipped at offset 575 Error in TBufferFile::CheckByteCount: object of class TH1 read too few bytes: 751 instead of 6934 Error in TBufferFile::CheckByteCount: object of class TH1D read too few bytes: 6944 instead of 6956 Error in TFileMerger::MergeRecursive: TKey and object retrieve disagree on type (GH1D vs TH1D). Continuing with TH1D. Error in TBufferFile::ReadClassBuffer: Could not find the StreamerInfo for version 7 of the class TNamed, object skipped at offset 65 Error in TBufferFile::CheckByteCount: object of class TNamed read too few bytes: 2 instead of 508 Error in TBufferFile::ReadClassBuffer: class: TAttFill, attempting to access a wrong version: 12002, object skipped at offset 575 Error in TBufferFile::CheckByteCount: object of class TH1 read too few bytes: 751 instead of 96534 Error in TBufferFile::CheckByteCount: object of class TH1D read too few bytes: 96544 instead of 96556 Error in TFileMerger::MergeRecursive: TKey and object retrieve disagree on type (GH1D vs TH1D). Continuing with TH1D. Error in TBufferFile::ReadClassBuffer: Could not find the StreamerInfo for version 7 of the class TNamed, object skipped at offset 65 Error in TBufferFile::CheckByteCount: object of class TNamed read too few bytes: 2 instead of 508 Error in TBufferFile::ReadClassBuffer: class: TAttFill, attempting to access a wrong version: 12002, object skipped at offset 575 Error in TBufferFile::CheckByteCount: object of class TH1 read too few bytes: 751 instead of 96534 Error in TBufferFile::CheckByteCount: object of class TH1D read too few bytes: 96544 instead of 96556 Error in TBufferFile::ReadClassBuffer: Could not find the StreamerInfo for version 7 of the class TNamed, object skipped at offset 65 Error in TBufferFile::CheckByteCount: object of class TNamed read too few bytes: 2 instead of 508 Error in TBufferFile::ReadClassBuffer: class: TAttFill, attempting to access a wrong version: 12002, object skipped at offset 575 Error in TBufferFile::CheckByteCount: object of class TH1 read too few bytes: 751 instead of 96534 Error in TBufferFile::CheckByteCount: object of class TH1D read too few bytes: 96544 instead of 96556 Error in TBufferFile::ReadClassBuffer: Could not find the StreamerInfo for version 7 of the class TNamed, object skipped at offset 65 Error in TBufferFile::CheckByteCount: object of class TNamed read too few bytes: 2 instead of 508 Error in TBufferFile::ReadClassBuffer: class: TAttFill, attempting to access a wrong version: 12002, object skipped at offset 575 Error in TBufferFile::CheckByteCount: object of class TH1 read too few bytes: 751 instead of 96534 Error in TBufferFile::CheckByteCount: object of class TH1D read too few bytes: 96544 instead of 96556 Error in TFileMerger::MergeRecursive: TKey and object retrieve disagree on type (GH1D vs TH1D). Continuing with TH1D. Error in TBufferFile::ReadClassBuffer: Could not find the StreamerInfo for version 4 of the class TH1, object skipped at offset 67 Error in TBufferFile::CheckByteCount: object of class TH1 read too few bytes: 2 instead of 548 Error in TFileMerger::MergeRecursive: TKey and object retrieve disagree on type (GH2D vs TH2D). Continuing with TH2D. Error in TBufferFile::ReadClassBuffer: Could not find the StreamerInfo for version 4 of the class TH1, object skipped at offset 67 Error in TBufferFile::CheckByteCount: object of class TH1 read too few bytes: 2 instead of 548 Error in TBufferFile::ReadClassBuffer: Could not find the StreamerInfo for version 4 of the class TH1, object skipped at offset 67 Error in TBufferFile::CheckByteCount: object of class TH1 read too few bytes: 2 instead of 548 Error in TBufferFile::ReadClassBuffer: Could not find the StreamerInfo for version 4 of the class TH1, object skipped at offset 67 Error in TBufferFile::CheckByteCount: object of class TH1 read too few bytes: 2 instead of 548 Error in TFileMerger::MergeRecursive: TKey and object retrieve disagree on type (GH2D vs TH2D). Continuing with TH2D. Error in TBufferFile::ReadClassBuffer: Could not find the StreamerInfo for version 7 of the class TNamed, object skipped at offset 65 Error in TBufferFile::CheckByteCount: object of class TNamed read too few bytes: 2 instead of 508 Error in TBufferFile::ReadClassBuffer: class: TAttFill, attempting to access a wrong version: 1002, object skipped at offset 575 Error in TBufferFile::CheckByteCount: object of class TH1 read too few bytes: 751 instead of 8534 Error in TBufferFile::CheckByteCount: object of class TH1D read too few bytes: 8544 instead of 8556 Error in TFileMerger::MergeRecursive: TKey and object retrieve disagree on type (GH1D vs TH1D). Continuing with TH1D. Error in TBufferFile::ReadClassBuffer: Could not find the StreamerInfo for version 7 of the class TNamed, object skipped at offset 65 Error in TBufferFile::CheckByteCount: object of class TNamed read too few bytes: 2 instead of 508 Error in TBufferFile::ReadClassBuffer: class: TAttFill, attempting to access a wrong version: 1002, object skipped at offset 575 Error in TBufferFile::CheckByteCount: object of class TH1 read too few bytes: 751 instead of 8534 Error in TBufferFile::CheckByteCount: object of class TH1D read too few bytes: 8544 instead of 8556 Error in TBufferFile::ReadClassBuffer: Could not find the StreamerInfo for version 7 of the class TNamed, object skipped at offset 65 Error in TBufferFile::CheckByteCount: object of class TNamed read too few bytes: 2 instead of 508 Error in TBufferFile::ReadClassBuffer: class: TAttFill, attempting to access a wrong version: 1002, object skipped at offset 575 Error in TBufferFile::CheckByteCount: object of class TH1 read too few bytes: 751 instead of 8534 Error in TBufferFile::CheckByteCount: object of class TH1D read too few bytes: 8544 instead of 8556 Error in TFileMerger::MergeRecursive: TKey and object retrieve disagree on type (GH1D vs TH1D). Continuing with TH1D. Error in TBufferFile::ReadClassBuffer: Could not find the StreamerInfo for version 7 of the class TNamed, object skipped at offset 65 Error in TBufferFile::CheckByteCount: object of class TNamed read too few bytes: 2 instead of 508 Error in TBufferFile::ReadClassBuffer: class: TAttFill, attempting to access a wrong version: 12002, object skipped at offset 575 Error in TBufferFile::ReadVersion: Could not find the StreamerInfo with a checksum of 0x0 for the class "TAttMarker" in hist_run0034_test.root. Error in TBufferFile::CheckByteCount: object of class TAttMarker read too few bytes: 6 instead of 1048576 Error in TBufferFile::CheckByteCount: Byte count probably corrupted around buffer position 575: 1048576 for a possible maximum of 96022 Error in TBufferFile::ReadBuffer1: class: TAttAxis, attempting to access a wrong version: 33, object skipped at offset 96617 Error in TBufferFile::ReadBuffer1: class: TAxis, attempting to access a wrong version: 16324, object skipped at offset 96635 Error in TBufferFile::ReadBuffer1: class: TAxis, attempting to access a wrong version: 32, object skipped at offset 96641 Error in TBufferFile::CheckByteCount: object of class TAxis read too many bytes: 2 instead of -1506509056 Warning in TBufferFile::CheckByteCount: TAxis::Streamer() not in sync with data on file hist_run0034_test.root, fix Streamer() Error in TBufferFile::CheckByteCount: Byte count probably corrupted around buffer position 96635: -1506509056 for a possible maximum of -34 Error in TBufferFile::CheckByteCount: object of class TH1 read too many bytes: 96633 instead of 96534 Warning in TBufferFile::CheckByteCount: TH1::Streamer() not in sync with data on file hist_run0034_test.root, fix Streamer() Error in TBufferFile::CheckByteCount: object of class TH1D read too few bytes: 96544 instead of 96556 Error in TFileMerger::MergeRecursive: TKey and object retrieve disagree on type (GH1D vs TH1D). Continuing with TH1D. Error in TBufferFile::ReadClassBuffer: Could not find the StreamerInfo for version 7 of the class TNamed, object skipped at offset 65 Error in TBufferFile::CheckByteCount: object of class TNamed read too few bytes: 2 instead of 508 Error in TBufferFile::ReadClassBuffer: class: TAttFill, attempting to access a wrong version: 12002, object skipped at offset 575 Error in TBufferFile::ReadVersion: Could not find the StreamerInfo with a checksum of 0x0 for the class "TAttMarker" in hist_run0035_test.root. Error in TBufferFile::CheckByteCount: object of class TAttMarker read too few bytes: 6 instead of 1310720 Error in TBufferFile::CheckByteCount: Byte count probably corrupted around buffer position 575: 1310720 for a possible maximum of 96022 Error in TBufferFile::ReadBuffer1: class: TAttAxis, attempting to access a wrong version: 33, object skipped at offset 96617 Error in TBufferFile::ReadBuffer1: class: TAxis, attempting to access a wrong version: 16324, object skipped at offset 96635 Error in TBufferFile::ReadBuffer1: class: TAxis, attempting to access a wrong version: 32, object skipped at offset 96641 Error in TBufferFile::CheckByteCount: object of class TAxis read too many bytes: 2 instead of -1506509056 Warning in TBufferFile::CheckByteCount: TAxis::Streamer() not in sync with data on file hist_run0035_test.root, fix Streamer() Error in TBufferFile::CheckByteCount: Byte count probably corrupted around buffer position 96635: -1506509056 for a possible maximum of -34 Error in TBufferFile::CheckByteCount: object of class TH1 read too many bytes: 96633 instead of 96534 Warning in TBufferFile::CheckByteCount: TH1::Streamer() not in sync with data on file hist_run0035_test.root, fix Streamer() Error in TBufferFile::CheckByteCount: object of class TH1D read too few bytes: 96544 instead of 96556 Fatal in TH1D::Merge: Fatal error merging histogram - bin number is 65537 and array size is 0 aborting

0 0x00007f34e69460ac in waitpid () from /lib64/libc.so.6

1 0x00007f34e68cb092 in do_system () from /lib64/libc.so.6

2 0x00007f34ea5620b2 in TUnixSystem::StackTrace() () from /usr/lib64/root/libCore.so.6.06

3 0x00007f34ea47fc11 in DefaultErrorHandler(int, bool, char const, char const) () from /usr/lib64/root/libCore.so.6.06

4 0x00007f34ea47f59a in ErrorHandler () from /usr/lib64/root/libCore.so.6.06

5 0x00007f34ea490e41 in TObject::Fatal(char const, char const, ...) const () from /usr/lib64/root/libCore.so.6.06

6 0x00007f34e97c71a0 in TH1::Merge(TCollection_) () from /usr/lib64/root/libHist.so.6.06

7 0x00007f34e9ec019c in TFileMerger::MergeRecursive(TDirectory, TList, int) () from /usr/lib64/root/libRIO.so.6.06

8 0x00007f34e9ebfde5 in TFileMerger::MergeRecursive(TDirectory_, TList*, int) () from /usr/lib64/root/libRIO.so.6.06

9 0x00007f34e9ec13fd in TFileMerger::PartialMerge(int) () from /usr/lib64/root/libRIO.so.6.06

10 0x00000000004026ce in main ()

Aborted

Lunderberg commented 8 years ago

It looks like there are multiple versions of root in play here. Could run make clean && make in the grutinizer directory and see if gadd works? It looks like something is being compiled against one version of root, then run against a different version.

placebosarah commented 8 years ago

I've tried the make clean/make a few times, but it doesn't seem to help here. I'll take a second look at my root version(s) though.

placebosarah commented 8 years ago

EDIT: I believe that most of these errors were due to the two versions of ROOT conflicting, but while removing the local version allows the GUI to run, gadd is still failing.

Okay, still having trouble with this. I've installed a local version of ROOT to compile against (the system version was scattered across several locations), which gave me a new error: "Error “gnu/stubs-32.h: No such file or directory” when running gadd (not when re-compiling the latest version of grutinizer). I then installed the 32-bit glibc-devel package to resolve this, however still having problems (gadd_error_3.11). Additionally, I'm unable to use the grutinizer gui (gui_error_3.11)

gadd_error_3.11.txt gui_error_3.11.txt

placebosarah commented 7 years ago

Could someone point me to the gadd source code? I'm not sure it's picking up on my dictionaries correctly as I've got some non-standard locations.

Thanks.

Lunderberg commented 7 years ago

At the moment, there is no gadd source code used directly. It is a direct copy of the hadd source code, located at $ROOTSYS/main/src/hadd.cxx, but with all references to hadd changed to gadd. The particular command that generates the gadd.o object file can be found in the makefile by searching for "gadd.o". This object file is then linked against all the grutinizer libraries.

The reason why it has this special behavior is so that it is compatible with both root5 and root6. Rather than needing to maintain two separate versions of gadd.cxx, one for root5 and one for root6, we just use whichever one is included with root.

pcbend commented 7 years ago

Hi Sarah,

I did not realize this was still an issue for what ever reason. What do you mean you have weird paths?

What are the outputs of:

root-config --version

root config --libs

root-config --cflags

echo $LD_LIBRARY_PATH

echo $PATH

?

On Thu, Dec 1, 2016 at 9:31 AM, Lunderberg notifications@github.com wrote:

At the moment, there is no gadd source code used directly. It is a direct copy of the hadd source code, located at $ROOTSYS/main/src/hadd.cxx, but with all references to hadd changed to gadd. The particular command that generates the gadd.o object file can be found in the makefile by searching for "gadd.o". This object file is then linked against all the grutinizer libraries.

The reason why it has this special behavior is so that it is compatible with both root5 and root6. Rather than needing to maintain two separate versions of gadd.cxx, one for root5 and one for root6, we just use whichever one is included with root.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/pcbend/GRUTinizer/issues/118#issuecomment-264187277, or mute the thread https://github.com/notifications/unsubscribe-auth/AAacI-Ma8nakMxpp8Zr4K9HNXY8IiwANks5rDtpRgaJpZM4KZ0I0 .

placebosarah commented 7 years ago

Hi Peter, The installation of ROOT on my work PC seems to be a bit scattered, but I think my paths should be correct:

bash-4.2$ root-config --version 6.06/08 bash-4.2$ root-config --libs -L/usr/lib64/root -lCore -lRIO -lNet -lHist -lGraf -lGraf3d -lGpad -lTree -lRint -lPostscript -lMatrix -lPhysics -lMathCore -lThread -lMultiProc -pthread -lm -ldl -rdynamic bash-4.2$ root-config --cflags -pthread -std=c++11 -Wno-deprecated-declarations -m64 -I/usr/include/root bash-4.2$ echo $LD_LIBRARY_PATH /scratch2/MSU/GRUTinizer/GRUTinizer/lib:/usr/lib64/root:/usr/local/lib:/usr/lib:/usr/local/lib64:/usr/lib64 bash-4.2$ echo $PATH /scratch2/MSU/GRUTinizer/GRUTinizer/bin:/opt/sge/bin:/opt/sge/bin/lx-amd64:/usr/lib64/qt-3.3/bin:/opt/mendeleydesktop/bin:/opt/matlab-R2015a/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/opt/pgi/linux86-64/15.5/bin:/opt/rw05-3:/usr/share/applications:/usr/share/applications:/usr/share/applications:/usr/share/applications:/usr/share/applications

placebosarah commented 7 years ago

Hi all, Thanks to Eric's pointer I've found the problem (hadd.cxx couldn't be found). Having got a copy and changed the reference in the makefile, gadd now seems to be working well. (How gadd managed to be generated when there's no sign of the .cxx I'm not sure, but there we go.)

Thanks for the help.