Readline on Mothur v1.9 - bug?

mothur bugs
1

I’ve been using mothur for a couple months without any problem, installing each new version and working ok. I use mothur on two machines: 1) At lab, we have a desktop DELL Precision 470, two processors, 4gb ram, running BioLinux 5 (Ubuntu 8.04, check @ http://nebc.nerc.ac.uk); 2) At home, HP Pavillion Dv5020 laptop, amd turion64, 2 Gb ram, running Fedora Core 10.

But after compile/installing mothur v1.9, on both Ubuntu and Fedora, I got some problem perheaps with the readline. Mothur v1.9 runs ok, does everything, but it doesn’t repeats the last command lines when I press “up arrow”, the same with right/left/down arrows. This sounds like an issue with my readline, not with mothur. Is anybody else having this problem?

openMPI and readline/readline5 libraries are installed on both linux systems, and I edited the makefile to set “yes” on using readline. The strange point is the fact in both Fedora and Ubuntu the arrows were working on v1.8, but not now on v1.9. :frowning:

I’m trying to solve this. Any ideas?

Thanks,

2

**Updating

On the laptop (Fedora), I have just re-compiled mothur v1.9 and the arrows are working. The only thing I did was to edit the makefile and set readline to “yes” (USEREADLINE ?= yes) and MPI to “no” (USEMPI ?= no), saved and recompiled. Setting both to “yes” seems to be the problem here. Does anyone got the same problem?

3

I am in a similar situation… See http://www.wiki.mothur.org/forum/viewtopic.php?f=3&t=397&p=882&sid=08a23e8a7e5ad30ff1e4308a293700e6#p882

4

Version 1.9 disables the readline feature if you enable mpi, because mpirun disables the readline features. This will be changed in 1.10.0, so if you run the mpi-enabled version without mpirun you can take advantage of the readline library. On a side note, if you are running mothur on a single machine the non-mpi enabled version runs faster than the mpi-enabled version.