COPY v. java performance comparison

I'm playing with various data models to compare performance and
practicalities and not sure if I should be surprised by the numbers I'm
getting. I hope this report isn't too wishy-washy for reasoned comment.

One model says a genotype is defined as follows:

Table "public.oldstyle"
+-------------+--------------+-----------+
| Column | Type | Modifiers |
+-------------+--------------+-----------+
| id | uuid | not null |
| sample_name | text | not null |
| marker_name | text | not null |
| allele1 | character(1) | |
| allele2 | character(1) | |
+-------------+--------------+-----------+
(0. id is a Primary Key)
(1. Take what you will from the table name.)
(2. I hadn't thought of "char" type at this point)
(3. Ultimately the names would become ids, RI included)
(4. We're loading 39 samples and ~950K markers)

I loaded 37M+ records using jOOQ (batching every 1000 lines) in 12+
hours (800+ records/sec). Then I tried COPY and killed that after 11.25
hours when I realised that I had added on non-unque index on the name
fields after the first load. By that point is was on line 28301887, so
~0.75 done which implies it would have take ~15hours to complete.

Would the overhead of the index likely explain this decrease in throughput?

Impatience got the better of me and I killed the second COPY. This time
it had done 54% of the file in 6.75 hours, extrapolating to roughly 12
hours to do the whole thing.

That matches up with the java speed. Not sure if I should be elated with
jOOQ or disappointed with COPY.

Btw, I can load the roughly the same data in to the model below in 10.5
seconds. It only adds 39 very wide lines. I haven't got to the
practicality bits yet :)

Table "public.chipcall"
+-------------+------+-----------+
| Column | Type | Modifiers |
+-------------+------+-----------+
| id | uuid | |
| sample_name | text | |
| chip_model | uuid | |
| gta | text | |
+-------------+------+-----------+

This just a dev desktop environment:
RHEL 6.5
PostgreSQL 9.3.1 on x86_64-unknown-linux-gnu, compiled by gcc (GCC)
4.4.7 20120313 (Red Hat 4.4.7-4 [hm, interesting contradiction]), 64-bit
2 QuadCore cpu MHz: 2925.878
The input file and postgres data are on separate disks, but only one
controller.

Thanks in advance, even if you only read this far.