two columns in pid output HDF5

From: Long Do Cao <docao_at_vega.ess.sci.osaka-u.ac.jp>
Date: Wed, 6 Aug 2014 15:06:07 +0900

Dear all gadget users,

I encountered a very strange problems in the output in HDF5 format on Gadget3. In the snapshot body, there are pos, vel, pid etc. While all variables containing 3 columns (e.g. pos) are perfectly ok, all variables which should contain only one column, actually have 2 ! For example, the pid variable has 2 columns in it. In other words, itís as if each particle had 2 pids. These numbers nor the couple is unique. Thus, the pid is completely out of control. The funny thing is that this problem occurs only when SnapFormat = 3. Everything works well when SnapFormat=1 (even though both used a binary with HAVEHDF5 enabled).

I was wondering if anyone has encountered this problem before. My guess is that itís either machine-related or compiler-related, because on another machine, the exact same code generates good snapshots.I also made sure I was using the same version of HDF5 static library (1.8.9) on both machines. I tried with version 1.6 and itís the same problem. Robert Thompson has left a message couple of days ago on the hdf5 forum with no solution so far.

http://hdf-forum.184993.n3.nabble.com/HDF5-writing-multiple-columns-when-there-should-only-be-one-td4027366.html



### How I compiled:
I basically followed instructions found on this page http://www.hpcadvisorycouncil.com/pdf/GADGET-2_Best_Practices.pdf. There is no complaint while compiling.


### Here are some details about the machine where it doesnít work:

-bash-4.1$ cat /etc/issue
CentOS release 6.2 (Final)
Kernel \r on an \m

-bash-4.1$ uname -a
Linux pluto.ess.sci.osaka-u.ac.jp
2.6.32-220.el6.x86_64 #1 SMP Tue Dec 6 19:48:22 GMT 2011 x86_64 x86_64 x86_64 GNU/Linux

-bash-4.1$ mpicc --version
gcc (GCC) 4.4.6 20110731 (Red Hat 4.4.6-3)

I attached the Makefile_pluto of gadget3.

Please let me know if you have an idea about this. Thank you by advance for your help.

Best,

Long




--------------------------------------------------------------
Long DO CAO (Office F617)
Office phone: +81 6-6850-5482
Osaka University, Graduate School of Science
Department of Earth and Space Science
1-1 Machikaneyama-cho
Toyonaka, Osaka, 560-0043, Japan
---------------------------------------------------------------
--------------------------------------------------------------
Long DO CAO (Office F617)
Office phone: +81 6-6850-5482
Osaka University, Graduate School of Science
Department of Earth and Space Science
1-1 Machikaneyama-cho
Toyonaka, Osaka, 560-0043, Japan
---------------------------------------------------------------
Received on 2014-08-06 08:06:36

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