Inefficient process and thread distribution to cores on multicore system

I am doing some scientific computations in Ubuntu on a multicore workstation. I will run a multi-threaded program using OpenMP and I want it to run fast. Currently I am testing and debugging this program and meanwhile I have some single-threaded processes running (which are computing auxiliary results). The problem is that Ubuntu distributes the processes and threads very inefficiently between CPU cores.

In the workstation, there is Intel Xeon W3680, which has six physical cores and hyperthreading, so there are 12 logical cores. I can understand if Ubuntu cannot recognize physical cores but I cannot understand why it is using almost only four logical cores. Example - I had five single-thread and one six-thread processes running and they were distributed to the cores this way:
* core 1: two single-thread processes and the six-thread process, i.e. 8 threads running on a single logical core,
* core 3: a single-thread process,
* core 4: a single-thread process,
* core 5: a single-thread process,
* remaining 8 logical cores: almost no load.
My observation is based on Gnome System Monitor and confirmed by the slowness of the processes running on the same core.

As these computations take whole days, it is quite important to run them efficiently. So what can I do? Should I install Debian? ;-) Well, I would appreciate a faster and simpler solution :-) .

Jan